The Hydrodynamics of Intermittently Closing and Opening Lakes … · VI 2.8 Summary 21 CHAPTER 3 22 VERTICAL MIXING PROCESSES IN INTERMITTENTLY CLOSING AND OPENING LAKES AND LAGOONS,

The Hydrodynamics of

Intermittently Closing and Opening

Lakes and Lagoons

Emma Jane Gale B.Sc. (Hons.)

This thesis is presented for the degree of Doctor of Philosophy

of the University of Western Australia School of Environmental Systems Engineering

2006

II

III

ABSTRACT

Coastal lagoons play an important role in the transport of materials between the

coastal zone and the ocean. Understanding the dynamics associated with the movement of

waters between and within these systems is therefore significant in defining the ecological

health of the system. An important sub category of lagoons is Intermittently Closing and

Opening Lakes and Lagoons (ICOLLs). These systems lack any significant river inflow; have

a restricted sill type inlet and experience intermittent exchange with the ocean, making them

susceptible to the retention of nutrients and pollutants from the catchment. The duration and

frequency of an opening event may vary from weeks to months between each ICOLL, and

inter and intra annually, respectively, and during an opening event, there are appreciable

fluctuations in water level (1-3m range) accompanied by large changes in salinity (7 – 30ppt)

within a short timeframe (hours). To date, a few ecological studies have been completed on

ICOLLs, yet no detailed studies of the mixing, circulation and exchange of the waters have

been undertaken. .

To examine the hydrodynamics, two ICOLLs, located in south-eastern Australia,

were chosen and examined as a comparative study due to their similar bathymetries yet

significantly different opening regimes. The research combined both field data analysis with

numerical modelling. The results revealed that different physical processes governed vertical

mixing/stratification in the two ICOLLs and the varying nature of the physical forcing, and

their interactions, generated changes on a variety of timescales (hours, days, and weeks).

Variations in the vertical mixing allowed the set-up and breakdown of stratification on a

short timescale (hours, days) and promoted the depletion of dissolved oxygen at depth once a

critical strength of stratification had been reached. The results also revealed that the

circulation and flushing characteristics were dominated by tidal and wind effects in both

IV

ICOLLs; however the exchange processes were different. The exchange in the smaller

ICOLL was dominated by tidal effects, whilst in the larger ICOLL, a fortnightly tide, defined

as spring tidal pumping or spring tidal set-up, dominated the exchange. Regardless of the

processes complete oceanic flushing was still predicted for each system, by the end of their

respective opening events. The modelling work successfully reproduced the spring tidal set-

up in water level and exchange, using real bathymetry and meteorological forcing and defined

the spring tidal set-up as the key predictable process in the exchange of water and salt

between the larger ICOLL and the ocean. It was also shown that strong winds had the

capacity to influence the magnitude of the exchange. The overall outcomes of this research

therefore include the identification of key physical processes associated with the variability of

the hydrodynamics within and between ICOLLs, which will aid in the future management of

these highly dynamic systems.

V

CONTENTS

ABSTRACT III

LIST OF FIGURES VIII

LIST OF TABLES X

ACKNOWLEDGEMENTS XII

PREFACE XII

CHAPTER 1 1

1.1 Motivation 1

1.2 Objectives 2

1.3 Structure of the thesis 3

CHAPTER 2 4

BACKGROUND INFORMATION 4

2.1 Coastal Lakes and Lagoons: definitions and classifications 4

2.2 Intermittently Closing and Opening Lakes and Lagoons (ICOLLs) 5

2.3 The hydrodynamics of ICOLLs 7

2.4 Vertical Mixing Processes and Stratification Dynamics 8

2.5 Circulation processes in ICOLLs 12

2.5.1 Sub tidal forcing in ICOLLs 14

2.5.2 Storm surges 14

2.5.3 Continental shelf waves 14

2.5.4 Inverted barometer effect 15

2.5.5 Internal sub tidal forcing 15

2.6 Exchange processes in ICOLLs 16

2.6.1 Flushing timescales of ICOLLs 18

2.7 Water quality in ICOLLS 20

VI

2.8 Summary 21

CHAPTER 3 22

VERTICAL MIXING PROCESSES IN INTERMITTENTLY CLOSING AND OPENING

LAKES AND LAGOONS, AND THE DISSOLVED OXYGEN RESPONSE 22

3.1 Abstract 22

3.2 Introduction 23

3.2.1 Study Area 24

3.3 Methods 27

3.3.1 Field Observations 27

3.3.2 Analysis methods 28

3.4 Results and Discussion 31

3.4.1 Closed state: summer conditions 31

3.4.2 Closed state: predicting the winter conditions 33

3.4.3 Open State: autumn 34

3.5 Concluding remarks 47

CHAPTER 4 49

PROCESSES DRIVING CIRCULATION, EXCHANGE AND FLUSHING WITHIN

INTERMITTENTLY CLOSING AND OPENING LAKES AND LAGOONS 49

4.1 Abstract 49

4.2 Introduction 49

4.3 Materials and methods 52

4.3.1 Field site descriptions 52

4.3.2 Data collection 53

4.3.3 Data Analysis 55


4.4.1 Tidal and wind forcing in Wamberal Lagoon 57

4.4.2 Oceanic exchange within Wamberal Lagoon 60

4.4.3 Tidal and wind forcing in Smiths Lake 63

4.4.4 Low Frequency forcing within Smiths Lake 66

4.4.5 Oceanic exchange within Smiths Lake 69

4.4.6 Flushing timescales for the two ICOLLs 72


VII

CHAPTER 5 77

THE IMPORTANCE OF SUB TIDAL PROCESSES ON THE FLUSHING AND

EXCHANGE OF AN INTERMITTENTLY OPEN SHALLOW COASTAL LAKE 77

5.1 Abstract 77

5.2 Introduction 78

5.3 Methods 80

5.3.1 Study site 80

5.3.2 The numerical model 81

5.3.3 Model set-up 82

5.3.4 Model Validation 82

5.3.5 Model scenarios 84

5.3.6 Quantifying the exchange 86


5.4.1 Salt wedge intrusion 87

5.4.2 Exchange characteristics 88

5.4.3 Flushing timescales 90

5.4.3.1 System wide flushing 90

5.4.3.2 Local Flushing 92

5.4.4 Variations in exchange and flushing 95


CHAPTER 6 98

CONCLUSIONS 98

6.1 Summary 98

6.2 Recommendations for future work 102

6.2.1 Transition between open and closed state 102

6.2.2 Rainfall Events 103

6.2.3 Spring tidal pumping 104

6.3 Final note 104

BIBLIOGRAPHY 105

VIII

LIST OF FIGURES Figure 2.1 Conceptual model of an ICOLL …………………………………… 6

Figure 2.2 A summary of the vertical mixing processes in ICOLLs………… 10

Figure 2.3 Strain induced periodic stratification……………………………... 10

Figure 2.4 Gravitational circulation ………………………………………… 13

Figure 2.5 Water levels in the Hawkesbury River, NSW……………………. 16

Figure 3.1 Location of the two field sites. …………………………………… 26

Figure 3.2 Time series of rainfall, water levels and wind data for Wamberal

Lagoon, May and June 2003 during the open-state ………………

35

Figure 3.3 Time series of offshore forcing tidal water level, density for Wamberal

Lagoon, during the open state, the individual energy contributions

and a summary of the mixing vs. stabilizing terms within Wamberal

Lagoon during the open-state ………………….

37

Figure 3.4 Horizontal water velocities and the energy derived from u3 during the

prospective flood tides at Wamberal lagoon during open-state.

38

Figure 3.5 Time series of Meteorological data for Smiths Lake, May – September

2003 …….. ……………………………………………

39

Figure 3.6 Time series of offshore forcing tidal data, density profiles within

Smiths Lake, individual forcing terms and a summary of the mixing

vs. stabilizing terms during the open-state ………………

40

Figure 3.7 Time series of density, dissolved oxygen and the Brunt -Vaisala

Frequency at Wamberal lagoon during open-state …………...…

43

Figure 3.8 Offshore tidal water levels and dissolved oxygen levels for Smiths

Lake during the open state.……………………………………….

46

Figure 4.1 The location of the two field sites, within Australia ……………... 54

Figure 4.2 Wamberal Lagoon mean velocity profiles ……………………….. 59

Figure 4.3 Time series of wind and mean salinity within Wamberal Lagoon, May

2003 ………………………………………………………..

60

Figure 4.4 Meteorological data and salt fluxes for Wamberal Lagoon, May 2003

……………………………………………………………….

63

Figure 4.5 Smiths Lake velocity profiles for July, 2003 …………………….. 65

Figure 4.6 Wind responses within Smiths Lake on the 17th July, 2003 ……... 66

Figure 4.7 Spectral density plots of water levels from Smiths Lake ………… 68

IX

Figure 4.8 Low pass filtered (25hrs) water levels for Smiths Lake ………….. 69

Figure 4.9 Meteorological data and salt flux for Smiths Lake, July 2003 …… 70

Figure 4.10 T-S plot of the surface and bottom waters within Smiths Lake, (16th

July - 10th August, 2003) and corresponding sea level heights

…………………………………………………………….

71

Figure 4.11 Smiths Lake (a) Sea Level heights, (b) mean salinity, and (c) Tidal

Exchange Ratio (TER) ……………………………………...

74

Figure 5.1 Smiths Lake, bathymetry, and model transect outputs (transects 1 and

2) and profile output locations (P1, P2 and P3) ………………

81

Figure 5.2 Model validations for Smiths lake (a) water levels from the model

output and the field data, (b) water level comparison, and (c) mean

hourly velocities from the field and the model output ……..

83

Figure 5.3 Boundary forcing for the scenario modelling: (a) Tidal forcing only,

(b) Sea level changes, and (c) observed variable wind climate

…………………………………………………………….

85

Figure 5.4 Salt wedge intrusion rates for (a) Tidal forcing only, (b) Tidal and sea

level changes, (c) variable wind, and (d) constant wind. ……..

87

Figure 5.5 Exchange fluxes for Smiths Lake (a) the spring neap tidal forcing, (b)

sub tidal water levels, (c) sub tidal water volume fluxes, and (d) sub

tidal salt fluxes, for all four simulations ………………….

89

Figure 5.6 System wide flushing times for Smiths Lake, under the four different

simulations ...…………………………………………...

91

Figure 5.7 Two west – east transects through Smiths Lake showing retention

times (in days) after 16 days in ……………………………….......

93

Figure 5.8 Tracer concentrations in the surface waters after 16 days …….. 94

Figure 6.1 Conceptual models of the physical forcing present within a) closed

and b) open ICOLL systems ………………………………

99

X

LIST OF TABLES

Table 3.1 The magnitude of the terms in equation (3.3) for Wamberal Lagoon

and Smiths Lake under closed conditions (Note: Wamberal Lagoon

and Smiths Lake data cover a period of 7 and 6 days respectively)

………………………………………………

33

Table 3.2 Summary of the two ICOLL states and implications for their

dissolved oxygen concentrations ………………………………... 48

Table 4.1 Harmonic Analysis of the tidal constituents within Wamberal

Lagoon, and the Ocean …………………………………………... 58

Table 4.2 Harmonic Analysis of tidal constituents with Smiths Lake and the

Ocean ……………………………………………………....... 64

Table 5.1 Different forcing combinations for the modelling

simulations……………………………………………………….. 85

XI

ACKNOWLEDGEMENTS

In the production of this thesis there are many people I wish to thank. Firstly I would

like to thank Professor Chari Pattiaratchi, my primary supervisor, at the University of

Western Australia, for his guidance and support throughout the last 4 years. I would also

like to thank Dr. Rosh Ranasinghe from the Department of Natural Resources in N.S.W.,

who was also my supervisor and provided guidance and support with often different, yet

equally important input. I would also like to thank the administration staff and Ruth

Gongora-Mesas.

I would like to extend a huge thank you to all the people who helped me with

fieldwork, including Jason Everett, Graham Gale, Stephen Gale, Peter Evans, Chari

Pattiaratchi, David Hamilton, Geoff Horn and Ben Russell. Without their help a large part

of this thesis would not have been possible. I would also like to thank Peter Evans and

Joanne Wilson, at the Department of Natural Resources in NSW, who provided me with in

kind support through the use of field equipment, deploying and retrieving instruments and

their communications and discussions on the topic of ICOLLs. I also wish to thank Iain

Suthers and Mark Baird, at UNSW, for extending their time and professional guidance. I

would like to thank the three examiners for providing helpful comments and advice, which

have made this thesis a more thorough piece of work.

On a more personal note I would like to thank Alicia Loveless for her support and

friendship throughout the years. Also my office mates Joanne O’Callaghan, Antwanet

Kostoglidis, Matt Eliot and Mun Woo and the postgraduates for providing a support

network. I also want to mention the rowing girls and the beer club crew for providing me

with many needed distractions throughout my PhD studies. Lastly, but not least, I wish to

thank my family, Graham, Pam and Stephen, and my husband Bruce, for their never-

ending support.

XII

PREFACE

Contained in this thesis are a number of manuscripts intended for journal

publication. These include the following:

Chapter 3 was published in Estuarine, Coastal and Shelf Science, titled as ‘Vertical

Mixing Processes in Intermittently Closing and Opening Lakes and Lagoons, and the Dissolved Oxygen

Response’ by Gale, E. Pattiaratchi, C. and Ranasinghe R., (2006) 69: 205-216

Chapter 4 has been accepted for publication by the Australian Journal of Marine and

Freshwater Research, titled ‘Processes driving circulation, exchange and flushing within Intermittently

Closing and Opening Lakes and Lagoons’ by Gale, E. Pattiaratchi, C. and Ranasinghe R.

Chapter 5 will be submitted to Estuarine, Coastal and Shelf Science, titled ‘The

importance of sub tidal processes on the flushing and exchange of an intermittently open

shallow coastal lake’ by Gale, E. Pattiaratchi, C. and Ranasinghe R.

Except where referenced the material presented in this thesis is a synthesis of my own

ideas and work undertaken by myself under the supervision of C. Pattiaratchi and R.

Ranasinghe. In addition, the fieldwork component was organised, managed and collected

by myself, except where stated, over the four years from 2002-2006. I also solely

undertook the numerical modelling by myself, with technical support from within the

department.

CHAPTER 1

1.1 Motivation

Small lakes, lagoons and estuaries are a common feature found along the south

east coast of Australia. Spending my childhood years growing up near one, for me they

are a feature synonymous with the beach life, a large tourism draw card and a huge

recreational facility that’s free for all ages and walks of life. Yet in the past and still

today, we are dredging the water bodies to make them bigger and to commercially sell

the sand, we are building training walls to maintain an opening, and we are loading

them with nutrients and pollutants from the catchments, and expecting them to cope,

without a detailed understanding of how they operate.

Coastal lakes and lagoons occupy 13% of coastal areas worldwide (Kjerfve

1994) and globally the coastal zone is under unprecedented pressure from various

human activities stemming from a population growth of c. 50% in the last 20 yrs (Roy

et al. 2001). They also play an important role in the transport of materials between the

coastal zone and the ocean, and understanding the dynamics associated with the

movement of waters between and within these systems is therefore significant in

defining the ecological health of the system.

Many coastal lagoons lack any significant river inflow and as a result they

experience intermittent exchange with the ocean, through a restricted type inlet. These

lagoons are known as Intermittently Closing and Opening Lakes and Lagoons

(ICOLLs), and they are extremely susceptible to the retention of nutrients and

pollutants from the surrounding catchment (Webster and Harris 2004). One

consequence of urban development is the practice of artificially opening ICOLLs to

increase flushing and reduce the threat of nearby flooding. As a result many ICOLLs

are maintained as open systems when, in fact, they would naturally be closed for long

THE HYDRODYNAMICS OF INTERMITTENTLY 2 CLOSING AND OPENING LAKES AND LAGOONS

periods of time (Dye and Barros 2005). Previous research by Jones and West (2005)

found that artificially opening the ICOLLs or carrying out other entrance works should

be done with great caution, as the related impact on the fish communities remains

largely unpredictable. Whilst Griffiths (2001) found that a shorter opening period to

the ocean may provide less opportunity for marine fishes to enter, and therefore

promote a more stable fish assemblage within the ICOLL. Documented fish kills

(Wilson et al. 2002) and occurrences of excessive algal and macro algae growth (Roy et

al. 2001), are further warnings that a more holistic approach is needed to manage these

systems, and that holistic approach comes with the knowledge of the hydrodynamic

processes, however to date, there have been no detailed studies undertaken on the

hydrodynamics of these systems.

1.2 Objectives

The aim of this research is to define the hydrodynamics of Intermittently

Closing and Opening Lakes and Lagoons through field measurements and numerical

modelling. This will be done by firstly examining in detail the vertical (mixing)

processes and then secondly examining the horizontal (circulation, exchange and

flushing) processes; in two contrasting systems. The third aim of the research is to

define the importance of the sub tidal processes by numerical modelling of one of the

ICOLLs. The discussion at the end of the thesis then examines the importance of this

work, and draws conclusions that may be applicable for the range of ICOLL systems

found along the south east coast of Australia and similar systems elsewhere in the

world.

GALE, E. PHD THESIS, UNIVERSITY OF WESTERN AUSTRALIA 3

1.3 Structure of the thesis

This thesis presents work undertaken using both field measurements and numerical

modelling. The main part of the thesis has been presented as a compilation of three papers

either in press or submitted to internationally peer reviewed journals. In chapter 2 the

background literature pertinent to the research is presented, with some useful definitions and

concepts that are used frequently in the following chapters.

In chapter 3 the first paper is presented. This paper was published in Estuarine, Coastal

and Shelf Science, titled as ‘Vertical Mixing Processes in Intermittently Closing and Opening Lakes and

Lagoons, and the Dissolved Oxygen Response’ by Gale, E. Pattiaratchi, C. and Ranasinghe R. In this

chapter the vertical mixing processes occurring within the ICOLLs are examined, and the

dissolved oxygen response is also investigated. This is a field-based study.

In chapter 4 the second paper is presented. This paper has been accepted for publication

by the Australian Journal of Marine and Freshwater Research, titled ‘Processes driving circulation,

exchange and flushing within Intermittently Closing and Opening Lakes and Lagoons’ by Gale, E.

Pattiaratchi, C. and Ranasinghe R. This paper examines the horizontal processes within the

two ICOLLs when they are open to the ocean and is also a field-based study.

In chapter 5, the third paper is presented. This paper has been submitted to Estuarine,

Coastal and Shelf Science, titled ‘The importance of sub tidal processes on the flushing and

exchange of an intermittently open shallow coastal lake’ by Gale, E. Pattiaratchi, C. and

Ranasinghe R. This paper utilizes a numerical model to examine the sub tidal process

operating within one of the field sites (Smiths Lake). The thesis finishes with chapter 6 where

the conclusions are presented in a summary format and some recommendations for further

research are noted.


CHAPTER 2

BACKGROUND INFORMATION

2.1 Coastal Lakes and Lagoons: definitions and classifications

Coastal lakes and lagoons can be classified as shallow coastal water bodies

separated from the ocean by a barrier, connected at least intermittently to the ocean by

one or more restricted inlets, and usually oriented shore parallel (Kjerfve 1994). The

water depth is typically 1-3 m, and almost always less than 5m, and they often exhibit

very high primary and secondary production rates, making them valuable resources for

the fisheries and aquaculture industries (Kjerfve 1994). The variation in entrance

dynamics allows a further classification into: choked, restricted and leaky lagoons, as

defined by Kjerfve (1994). Choked lagoons may also be defined as ephemeral estuaries

(Roy 1984) of which there are two sub classes: Intermittently Closing and Opening

Lakes and Lagoons (ICOLL) and Seasonally Open Tidal Inlets (SOTI). Both of these

estuarine systems are open, either by natural or artificial means, to the ocean at irregular

(ICOLL) or regular (SOTI) intervals. Some examples of ephemeral systems are

Honaver, Krishnapatam and Ponnani estuaries in India (Bruun, 1986); Wilson, Irwin

and Parry Inlets in Western Australia (Ranasinghe and Pattiaratchi, 1999); Narrabeen

and Wollumboola lagoons in New South Wales, Australia (Gordon, 1990); Hilsboro,

Jupiter and Lake Worth Inlets in Florida, USA (Stauble, 1993); and, Chilaw lagoon in

Sri Lanka (Wikramanaike and Pattiaratchi, 1999). Further examples of these systems

may be found throughout the world.


2.2 Intermittently Closing and Opening Lakes and Lagoons (ICOLLs)

Intermittently closing and opening lakes and lagoons refer to those coastal water bodies

that, for a combination of climatic and other reasons, become isolated from the sea for

periods at a time (Roy et al. 2001). Both the term ‘lake’ and ‘lagoon’ are included in the

term ICOLL, with the definition of ‘lake’ more commonly applied to the larger ICOLLs

whilst the tdefinition of lagoon is more commonly applied to the smaller ICOLLs, however

there are exceptions. Throughout this thesis the individual terms of lake and lagoon are

retained, as it applies to the official names of the field sites, however the terms lake and

lagoon may be used intrchangebly when examining concepts, discussions and conclusions.

ICOLL’s occur in microtidal, wave dominated coastal environments, and they have

small catchments and negligible river inflow which allows the mouth of the lagoon to

become blocked for the majority of the time. Winds cause mixing and some transport in

the larger lakes. Under most conditions the lake waters are saline to brackish but non tidal

and normal freshwater inputs are accommodated by evaporation and percolation through

the porous sand barrier. After heavy rains the beach berm is breached by storm waves and

/ or raised water levels (Roy et al. 2001) and the water body experiences tidal exchange.

ICOLLs are generally found in climatic regions which experience highly variable yearly

rainfall, the resulting unpredictability of the rainfall promotes the intermittent and erratic

opening regime (Roy et al. 2001), resulting in large variations in salinity and water levels

over a short timeframe (hours to days). The flushing is often poor due to the choked inlet

which can reduce the tidal range within the lake or lagoon to 10% of the ocean range

mainly due to frictional energy losses (Bruun 1994; Ranasinghe and Pattiaratchi, 1999). The

limited tidal exchange can also lead to wide fluctuations in salinity (Roy 1984), and the lake

then becomes tidal for weeks to months until open ocean processes reform the beach berm

across the inlet.


Along the southeast coastline of Australia, there are over 130 water bodies larger than

0.5 km2 in area (Roy et al. 2001), and of these, 60 (45%) are intermittently opening and

closing systems. Within this category 72% of the intermittently opening and closing systems

are artificially opened (DNR, 2002) either to mitigate nearby flooding, relieve poor water

quality or for navigational purposes. The result is that the opening quite often occurs below

the natural breakout level (Roy et al. 2001). Community disagreement often exists as to

whether the lake or lagoon should be artificially opened or not.

Figure 2-1 Conceptual model of an intermittently closing and opening lagoon (after Ryan et al 2003)

Previous research on ICOLL systems has largely focused on the ecology; with limited

research being undertaken on the physical process. Haines et al. (2006) developed a

morphometric classification scheme to assess the natural sensitivity of ICOLLs to


anthropogenic changes and their external inputs. One of the outcomes was an ‘Evacuation

Factor’ calculation, which measured how efficiently an ICOLL could remove pollutants

through tidal flushing. This research found that many ICOLLs were poorly flushed and that

the evacuation factor or flushing time was important for defining the ecological health of the

system. Rissik et al. (2003) also examined the flushing timescales of two ICOLLs, using a two

dimensional model, which highlighted the need to understand the potentially large spatial

variation in flushing, as well as the timescale. Research by Spooner and Spigel (2005)

identified that freshwater inflows had an immediate effect in promoting stratification within

an ICOLL, and successfully modelled this with a two dimensional numerical model and

Webster and Harris (2004) highlighted the importance of these rainfall events, in providing

nutrient rich inflows to the ICOLLs, which had the ability to change the ecological state.

From a more direct ecological view point, Jones and West (2005) compared the fish

dynamics in an artificially open ICOLL vs. a predominantly closed ICOLL and discovered

that the fish dynamics were quite sensitive to changes in the opening regime, and suggested

that further work may be needed to clarify why this was the case, and investigations by

Wilson et al. (2002) of a fish kill event in an ICOLL, suggested that the condition (physical

and ecological) of the ICOLL may be critical to its ecological health after an opening event.

This research illustrates some of the direct and indirect links, already seen, between the

mixing, circulation and flushing characteristics and the ecology of an ICOLL.

2.3 The hydrodynamics of ICOLLs

The hydrodynamics of ICOLLs cover processes that are found in both permanently open

estuaries and permanently closed lakes and are driven by wind, tides, precipitation,

evaporation and surface heat fluxes (Kjerfve 1994). However the circulation and mixing

characteristics of ICOLLs in the open state are different to those of permanently open

estuaries primarily because they have little river inflow or runoff from land and they are


located where the tidal range is small and the closed state hydrodynamics are different to

those of permanently closed lakes due to the large variations in salinity. An extra complexity

is added when trying to understand the hydrodynamics of an ICOLL system, due to the

dynamically changing water levels and the status of the inlet (closed or open). The resulting

processes driving the hydrodynamics can be broken into vertical and horizontal processes,

although they are not mutually exclusive. Whilst some of the processes may become more or

less significant between the open and closed state in the coastal lagoons, all relevant

processes will be addressed in the following sections.

2.4 Vertical Mixing Processes and Stratification Dynamics

Vertical mixing is a key process in rivers, lakes and estuaries (Fisher et al. 1979).

Therefore understanding the development and breakdown of vertical stratification/ de-

stratification cycles in a shallow water body is crucial in understanding the vertical fluxes of

water properties such as heat, salt, momentum and nutrients (Simpson et al. 1990). The

occurrence of vertical stratification is dependent upon the presence of density gradients,

where solar heating and/or the lateral advection of bouyancy due to freshwater inputs are

the main stratifying mechanisms (Fischer et al. 1979; Simpson et al. 1990). Vertical mixing

of water masses can be driven by turbulence generated at the bed (tidal mixing), turbulence

generated by shear at the thermocline / halocline, turbulence generated at the surface

(wind) (Fisher et al. 1979 ) and breaking of internal waves (Figure 2.2). Unstable density

gradients, driven by cooling or evaporation, may also promote vertical mixing.

Wind is usually the dominant source of mixing energy in large lakes, the open ocean

and some coastal areas, but in estuaries it may or may not play a large role (Fischer et al.

1979). Results of most estuarine studies show that tidal stirring at the bed, is the main

mixing mechanism. Due to the choked inlet, tidal velocities in ICOLLs may be expected to


be significantly less than those in a permanently open estuary and this will influence the

degree of vertical mixing. Ranasinghe and Pattiaratchi (1999) have shown that in Wilson

Inlet (WA), a SOTI, there are two distinctive behavioural patterns during winter and

summer which are largely unaffected by the tidal state, as in permanently open estuaries.

Variations in the tidal stirring can also lead to short periods of stratification defined as

Strain Induced Periodic Stratification (SIPS). This process occurs when the tidal amplitudes

are smaller (neap tides), producing a decrease in mixing. The decrease in mixing energy

reduces the ability of the turbulence to mix the whole water column and the associated tidal

straining, between the surface and bottom waters (Figure 2.3), on the ebb flow, can

promote a two layered flow. Upon the return flood tide, the process reverses and the water

column becomes well mixed again (Simpson et al. 1990). This is typical of systems where

the influence of freshwater is relatively weak and tidal mixing can usually easily overcome

any temporary stratification that may form.

During periods when the ICOLL is closed from the ocean, the salinity and water

levels are relatively stable (Lugg 1996), and tidal mixing is absent. Current literature

suggests that vertical mixing may be dominated by local winds, however unstable density

gradients, driven by cooling or evaporation, may also promote vertical mixing. The

presence of stratification is generally dominated by diurnal heating and cooling dynamics

(Fischer et al. 1979).


Figure 2-2 A summary of the vertical mixing processes in ICOLLs

Figure 2-3 Strain induced periodic stratification a) at the beginning of the ebb tide the outflow is vertically well mixed, b) halfway through the ebb tide the surface flow moves slightly faster due to being less dense and differential displacement promotes short periods of stratification (after Simpson et al. 1990)


Current theories provide diagrams and equations to define whether a water body is

vertically mixed or stratified, and Uncles (2002) provides a good overview on these. Some

of the more common methods include the Hansen and Rattray diagram (1966), and the

gradient Richardson number (Dyer 1997) both of which utilize the existing properties of

the water body to describe the current state, however they do not lend extensive insight

into the processes driving the particular hydrodynamic state.

One method of examining the stratification dynamics is to examine the potential

energy balance (Simpson et al. 1990) of the water column. This has proven to be useful in

defining the mixing and stratification dynamics in a variety of systems, from estuaries (Nunes

et al. 1989; Ranasinghe & Pattiaratchi 1999) to coastal seas (Rippeth & Simpson 1996; Lund-

Hansen et al. 1996), whilst also identifying the processes contributing to the dynamics. The

assumption is that processes that input potential energy, work towards stratifying the water

column, and processes that input kinetic energy, work towards de-stratifying the water

column (Simpson et al. 1990). The resulting potential energy of the water column can then be

defined as the potential energy anomaly, Ф, as follows:

( )zdzHg

H∫

−

−=Φ0

ρρ (2.1)

where

∫−

=0

)(1

h

dzzh

ρρ (2.2)

where, g is the acceleration due to gravity (m s -2), ρ is the water density (kg m-3), h is the water

depth (m) and z is the depth interval (m). The rate of change in the potential energy anomaly

⎟⎠⎞

⎜⎝⎛

dtdφ can then be examined to define whether the system is likely to remain well mixed or

become stratified. Defining the processes contributing to the energy balance does this. The


timing and magnitude of these processes may also become critical in defining whether the

water column is vertically mixed or stratified, and terms may be added or removed, as the

situation changes.

2.5 Circulation processes in ICOLLs

The circulation of water and solutes in estuaries and coastal lagoons are largely

governed by the mean flow, which is driven by pressure gradients. The pressure gradient

(equation 2.3) can be decomposed into two components: the first of these is baroclinic and

the second is barotropic (Hearn 1995):

dxdgdz

dxdg

dxdp

s

z ξρρ

ξ

−= ∫−

(2.3)

where p is pressure, sρ is the density at the sea surface, ξ is the surface elevation above a

datum level, and all other terms have been defined previously. The first term on the right

hand side represents the baroclinic component, which is driven by changes in density and can

be produced by variations in salinity or temperature. The second term represents the

barotropic component, which provides the net flux of fluid movement and controls the

changes in the volume of water in the lagoon (Hearn 1995).

In many closed lake systems, temperature gradients are the largest contributor to the

baroclinic component and may be produced by uneven heating of the water column. This

process is defined as convective circulation and can occur during the day when shallower

waters absorb more heat per unit volume than the deeper parts, leading to a horizontal

pressure gradient that drives a circulation (Farrow and Patterson, 1993). For most

permanently open estuarine systems though the density changes are typically caused by


variations in salinity between the river and the ocean. Within the region where estuary water

meets ocean water, the interaction produces a tidally averaged, two layered, circulation

pattern that is defined as gravitational circulation, (Figure 2.4) (Dyer 1997), combining both

barotropic and baroclinic components.

Figure 2.4 Gravitational circulation, where variations in water level, ξ, (Barotropic component) and variations in density, ρ, (Baroclinic component) promote a circulation set-up defined by the velocity profile, u (z) (after O’Callaghan 2005)

On a semi-diurnal timescale the propagating tidal wave entering the estuary or lagoon

produces spatial variation in the water surface elevation (Lewis 1997), which promotes flow.

Whilst on a longer timescales (days) variations in mean sea level will also promote a pressure

gradient resulting in a flow.

Barotropic flow may also be a consequence of local wind forcing. The

characteristically large surface area to depth ratio within shallow lagoons and estuaries can

promote a setup effect where the difference in water level drives a return flow (Smith 2001).

If there is an appreciable depth gradient at right angles to the wind, a horizontal circulation

may also develop (Groen 1969), promoting three dimensional circulation patterns. Whilst

these processes are known to be significant at a tidal timescale, sub tidal forcing may also be

present.


2.5.1 Sub tidal forcing in ICOLLs

In coastal lagoons with a restricted inlet, the tidal forcing may be dampened and sub tidal

forcing may become dominant (Holloway 1996). Sub tidal forcing can be described as any

forcing acting on a timescale longer than the tidal cycle (> 25 hrs), and encompasses local

forcing such as wind, and remote forcing including variations in the mean sea level driven by

storm surges, continental shelf waves and the inverted barometer effect. At the local scale,

the drag of the wind on the water surface can promote appreciable changes in the water

levels (Pugh 2004), however it is often the remote forcing that is more effective at promoting

sub tidal motions (Wong 1991).

2.5.2 Storm surges

Sub tidal motions are primarily driven by pressure gradients between the estuary / lagoon

and the ocean. Storm surges, promote relatively short term changes in mean sea level and are

normally attributed to the local effects of wind stress and atmospheric pressure (Provis and

Radok 1979). These are generally infrequent events associated with individual storms (Provis

and Radok 1979). The periodicity of weather systems along the south east Australian

coastline is approximately 9.5 days in summer and 4.5 days in winter (Krause and Radok

1976).

2.5.3 Continental shelf waves

In shallow continental shelf waters the wind stress can generate substantial currents in a

day or so, and as the winds change in direction and magnitude they accelerate continental

shelf waters to flow along the coast (Middleton 1995). The current pulses forced by the


synoptic-scale winds propagate in a wave-like manner along the continental shelf with the

coast to the left of the direction of propagation and these current pulses are called continental

shelf waves or coastal trapped waves (Middleton 1995). On most Australian shelves there are

mixed contributions of locally wind-forced shelf waves and freely propagating shelf waves

(generated by wind-forcing farther upstream in the sense of continental shelf wave

propagation) (Middleton 1995). Holloway (1996) noted that these waves had a periodicity of

around 6 days on the south east Australian coastline, however weather patterns change on

both seasonal and synoptic (one to three weeks) time scales, therefore the periodicity may

vary.

2.5.4 Inverted barometer effect

The inverted barometer effect refers to variations in the water level driven by changes in

atmospheric pressure. If the level in a mercury barometer increases, the sea levels are

depressed and vice versa (Pugh 2004), for example, an increase in atmospheric pressure by 1

millibar will produce a theoretical decrease in sea level by 1 cm. Due to this fact, the rsponse

can be separated from the effects of wind stress (Paraso and Valle-Levinson 1996).

2.5.5 Internal sub tidal forcing

In shallow waters, frictional resistance becomes the dominant physical process over most

of the tidal cycle (Pugh 2004) and this promotes greater sub tidal variations in water level

than the tides. During spring tides, the time taken for the water to drain away after high

water, under gravity, becomes longer than the tidal periods themselves, with the result that

long term pumping up of mean water levels occurs over spring tides (Pugh 2004). During

neap tides, the amplitudes and therefore duration of the high water is smaller, resulting in


greater frictional resistance and resulting in lower overall water levels. This produces a

fortnightly tide, which is an important secondary mechanism of mass movement of water

along the estuary (DNR 2006). This has been observed in lagoons (Hill 1994) and the upper

reaches of some estuaries (DNR 2006, Figure 5). The fortnightly tide has recently been

documented by Hinwood et al. (2005) as Spring Tidal Pumping (STP), reflecting the link of

the fortnightly water level variation with the spring neap tidal cycle. In the following chapters

this process will be defined as spring tidal setup, so as not to confuse the term with the

entirely separate process of tidal pumping. In a tidal analysis, this effect also shows in the Msf

constituent (Pugh 2004).

Figure 2.5 Fortnightly mean water level variation found in the upper reaches of the Hawkesbury River, N.S.W. Australia (after DNR, 2006)

2.6 Exchange processes in ICOLLs

To quantify the exchange between the lagoon and the ocean, salinity, which acts as a

conservative tracer, can be used as an indicator of transport. In an estuarine environment the

overall principle of a salt budget is that over many tides, any variations in river flow can be

ignored and the salinity at any particular point along the estuary will remain constant (Lewis

1997). Whilst the results are strictly only applicable to the salinity distribution, they can

indirectly also provide information on the transport of particles within the water (Dyer 1997).


A salt flux may be calculated for a single representative point in a channel, and this assumes

that there is no cross sectional variability or if enough data exists the salt flux may be

calculated for the whole cross section. The instantaneous rate of transport of salt, through a

unit width of a section, perpendicular to the mean flow is given by Dyer (1997) as:

∫ ==h

ushusdzQ0

(2.4)

where h is the depth, u is the observed velocity and s is the observed salinity. The < >

brackets represent time averaged values over one complete tidal cycle (flood and ebb tide). At

any depth uuu ′+= , where u is the depth averaged mean and u′ is the irregular, turbulent

variation. u may also be decomposed into Tuuu += , where Tu is the deviation with

mean depth from the mean tidal cycle depth u . The same theory can be applied to salinity,

s, and by combining the decomposed terms, substituting into equation 4, and integrating the

flux over a complete tidal cycle, the net flux can be calculated (Restrepo and Kjerfve 2002):

suhuhsshushusuhF TTTTTT ′′++++= (2.5)

(1) (2) (3) (4) (5)

The advective flux (term 1) is due to the mean tidal flow and is associated with the

change in storage during the tidal cycle, where a net emptying of the system suggests an

export in salt and vice versa. Term 2 represents tidal pumping, and refers to the net transport

of particles by oscillatory tidal currents over a tidal cycle and is usually directed upstream.

This flux usually reaches a maximum when currents and concentrations are in phase and is

usually the major landward flux component in well-mixed systems (Restrepo and Kjerfve

2002). Term 3 represents the cross correlation between tide and salinity, which represents any


time lag in change in salinity associated with a change in height. Term 4 represents the

Stoke’s drift dispersion, and accounts for the dispersion of salt related to the net drift of

water in the direction of wave travel (Masselink and Hughes 2003). Term 5 represents the salt

dispersion due to mean shear produced by the presence of gravitational circulation.

2.6.1 Flushing timescales of ICOLLs

A first order description of transport is expressed as ‘residence time’ or ‘flushing

time’, which is conceived as a measure of water mass retention time within defined

boundaries (Monsen et al. 2002). It is also one of the most important quantities relating the

physical processes to the ecology of estuarine systems (Geyer at al. 2000). Luketina (1998)

examines many of these methods in greater detail. A common mechanism for calculating the

flushing timescale of an estuarine system is to use the tidal prism method. In its simplest

form the tidal prism method is a calculation of the high tide volume divided by the tidal

prism volume (Dyer 1997):

TP

PVTF+

= (2.6)

where T = the tidal period, V is the low tide volume of the water body and P is the inter tidal

volume. There are however several assumptions with this method. Firstly, the system is well

mixed and that the water mass that enters the basin on a flood tide does not simply leave on

the following ebb (Hearn 1995). Secondly, the water leaving on the ebb does not return on

the following flood. Thirdly, the river flow is negligible, and finally, the system is in a

relatively steady state (Monsen et al. 2002). For these reasons the tidal prism method tends to

under estimate flushing times (Dyer 1997). More sophisticated estimation methods have been

derived from the tidal prism method, which incorporate the degree of mixing during the


flood tide. These methods require greater knowledge of the system and assume that the

degree of mixing is known.

If the degree of mixing is not known, it can be calculated using salinity. The Tidal

Exchange Ratio (TER), as described by Fischer et al. (1979), calculates the ratio (R) of new

water versus the total water entering the lake on the flood tide and can be calculated as:

( )( )eo

ef

SSSS

R−

−= (2.7)

Where Sf = the average salinity of water entering the estuary on the flood tide, Se = average

salinity of water leaving the estuary on the ebb tide, and So = the salinity of the ocean water.

Some caution is needed when applying this method to systems that have variable freshwater

inflow, as the lagoon water reaches the salinity of the ocean, the TER reaches zero, even

though exchange of new waters may still be occurring.

Methods that can be used to assess the localized flushing of a water body include age and

residence / retention time. Age is defined as the time a water parcel has spent since entering

the water body through one of the boundaries (Monsen et al. 2002) and residence / retention

time is the time it takes for any water parcel to leave the water body through its outlet to the

sea (Monsen et al. 2002). These methods are more intensive and require the release of

drogues, drifters, dye or similar into a water body. In the absence of detailed field data, or to

obtain a more accurate result, numerical models offer one of the best means to estimate local

flushing timescales.

In a numerical model the flushing time can be estimated as the time for a tracer mass

to reduce to a certain level of the initial mass (e.g. 1/e), this is often termed as the e-folding

time (Choi and Lee 2004). As the tracer mass decrease with time, an exponential decay is

assumed and an exponential curve can be fitted to the data to predict the flushing timescale:


teY βα= (2.8)

where Y is the percentage of original lake water (tracer mass), α and β are constants and t is

time in days.

2.7 Water quality in ICOLLS

Dissolved oxygen is an important factor in maintaining an ecologically healthy aquatic

ecosystem, and when levels drop below 6mg/L (ANZECC guidelines); the ecological health

of the aquatic system is compromised. The processes affecting dissolved oxygen

concentrations in aquatic ecosystems include atmospheric reaeration, photosynthesis and

respiration, oxidation of organic and inorganic matter, sediment oxygen demand and

nitrification (Gurel et al. 2005). Many of these processes are intricately tied to the

hydrodynamics and therefore the first step in identifying the potential for low dissolved

oxygen content in the waters of many aquatic systems may be to gain a greater understanding

of the hydrodynamics. For example, under persistent stratification the promotion of an

environment low in dissolved oxygen (D.O.) can initiate sediment-water column exchanges

(Webster and Harris 2004). Any nutrients that are released from the sediment, in the low

D.O. environment, can then be re-distributed into the water column upon de-stratification,

and can initiate phytoplankton blooms. However, on a shorter temporal scale, periodic

stratification events have been shown not to increase the likelihood of phytoplankton

blooms, over that of a constantly un-stratified water column (Lucas et al. 1998). In some

instances dissolved oxygen stratification also occurs in conjunction with slight temperature

stratification (Roy et al. 2001). This can be further enhanced during periods of non-mixing


when nutrients released from bottom sediments stimulate phytoplankton and algal growth in

surface waters (Roy et al. 2001). Therefore an understanding of the temporal scale of the

mixing dynamics is very important in understanding the dissolved oxygen response within an

aquatic system.

2.8 Summary

The variety of processes discussed here, and in previous research on similar lagoon

and estuarine systems, has shown that each lake or lagoon system can be quite dynamic and

driven by different processes. The combination of the processes and the significance of each

process at different timescales therefore make each system unique. The following work in

this thesis investigates these processes and identifies their significance within ICOLL systems.


CHAPTER 3

VERTICAL MIXING PROCESSES IN INTERMITTENTLY CLOSING

AND OPENING LAKES AND LAGOONS, AND THE DISSOLVED

OXYGEN RESPONSE

3.1 Abstract

Intermittently Closed and Open Lakes and Lagoons (ICOLLs) are located on micro-tidal

coasts (max. tidal range < 2 m) in temperate, tropical and sub tropical regions where the

annual rainfall is non-seasonal. ICOLLs are generally shallow (< 5 m depth) and are closed

to the ocean due to the formation of an entrance bar for the majority of the year, when

rainfalls are low. After periods of heavy rainfall, the super elevated water levels result in the

natural or artificial breaching of the entrance bar. Due to their small size and absence of

significant river inflows, ICOLLs exhibit strong temporal variations in their vertical density

gradients, which can result in episodic density stratification. Such episodic stratification

events may result in deterioration of the water quality including toxic algal blooms. This

paper presents results of field studies undertaken to determine the physical processes

governing vertical mixing/stratification in ICOLLs and their implications on dissolved

oxygen dynamics. Data from two contrasting ICOLLs located along the south-eastern

coastline of Australia; (a) Wamberal lagoon a small, shallower (~ 2m max depth) frequently

open ICOLL; and, (2) Smiths Lake, a larger, deeper (~5m max depth) infrequently open

ICOLL, are presented. The results indicated that Wamberal Lagoon was susceptible to

periods of stratification during both the closed and the open states. During the closed state,

periods of rainfall, low wind and/or high solar insolation led to short (< 3 days) and irregular


stratification events, whilst during the open state, stratification events occurred through a

combination of rainfall, low winds and variations in tidal mixing. There was a tendency for

dissolved oxygen to decrease, in the bottom waters, when the Buoyancy frequency was > 0.1

s-1. Smiths Lake demonstrated higher vertical stability and exhibited a tendency for persistent

stratification, during both the closed and open states, primarily due to solar insolation (closed

state) and gravitational circulation (open state), respectively. The persistent stratification

maintained a vertical gradient in dissolved oxygen between the surface and bottom layers.

However, tidal pumping associated with fortnightly tides appears to promote isolation of the

bottom waters, causing the dissolved oxygen rates to temporarily decrease (for approximately

5 days) during the neap cycle.

3.2 Introduction

Intermittently Closed and Open Lakes and Lagoons (ICOLLs) fall into the category of

intermittent estuaries (Roy et al. 2001) and are characterised by negligible river inflow. The

general bathymetry consists of a rounded main basin connected to the ocean by a narrow

inlet channel that impedes tidal exchange (Roy et al. 2001). ICOLLs are generally shallow (<

5 m depth) and are often found on micro-tidal coasts (spring tidal range < 2 m) in temperate,

tropical and subtropical regions of the world where the annual rainfall lacks seasonality. The

highly variable rainfall allows the lake or lagoon to become isolated from the ocean by a

beach barrier for the majority of the year. After periods of heavy rainfall, the water levels

become super elevated and the ICOLL opens to the ocean. The opening event may be

natural or artificial and can promote appreciable changes in water level (~ 1.5 m) and salinity

(7 – 30ppt) over a short time frame (hours) (Pollard 1994). Because the opening event is

driven by climatic conditions, the frequency and duration of the opening regimes can vary

within and between each ICOLL system. Some of the regions where intermittent estuarine


systems are found include: South Africa (Largier et al 1990), the east coast of South America

(Suzuki et al 1998), the south west (Ranasinghe and Pattiaratchi 1999) and the south east

coast of Australia (Dye and Barros 2005) as well as the coasts of the Americas (Bonilla et al.

2005).

Along the southeast coastline of Australia there are over 135 estuaries of which 45% are

intermittently open (Pollard 1994). The majority of the remaining 55% are kept permanently

open by training walls and breakwaters, primarily to provide boating access, but also to

maximize flushing and improve water quality (Roy et al. 2001). Within the sub category of

intermittently opening estuaries approximately 72% are artificially opened (DNR 2003).

Previous research on ICOLL systems has focused on the nutrient dynamics and water

chemistry, sea grass studies, phytoplankton dynamics and the fish populations (Dye and

Barros 2005). However, the hydrodynamic processes (e.g. vertical mixing, horizontal and

vertical circulation, flushing etc) that governs these ecological processes, which in turn

govern ICOLL water quality and health, have not been rigorously investigated to date.

Therefore, in order to develop and implement sustainable estuary management plans, it is

imperative that the hydrodynamic processes governing estuarine water quality and their

implications on dissolved oxygen dynamics be properly understood. This study focuses on

one such dominant hydrodynamic process; vertical mixing and stratification. The specific

aim of the study is to gain insight into the physical processes governing vertical

mixing/stratification in ICOLLs and the dissolved oxygen response.

3.2.1 Study Area

Smiths Lake and Wamberal lagoon, both located along the southeastern coastline of

Australia (Figure 3.1) were selected as case studies. The two sites were carefully selected to

investigate the vertical mixing and dissolved oxygen dynamics of the two main types of


ICOLLs; large, deep, infrequently open ICOLLs and small, shallow, frequently open

ICOLLs. From the two sites selected, Smiths Lake represents the former type while

Wamberal lagoon represents the latter. The two systems are similar in most other aspects,

including morphology and climate. The local climate at both sites is temperate with an

average annual rainfall greater then 800 mm with no marked seasonality. Both systems are

characterised by an absence of a major point source of freshwater input (i.e. a river) hence

the freshwater input to the system is through a diffuse system and is limited to rainfall and

runoff from the immediate periphery of the system. The ocean tides are semi-diurnal and

micro-tidal (spring tidal range < 2 m). The predominant winds are southerly and westerly,

associated with the passage of large atmospheric pressure systems over the east coast of

Australia (Roy et al. 2001). Strong onshore sea breezes also occur in summer.

Wamberal Lagoon (Figure 3.1) is located approximately 90 km north of Sydney, Australia

and has a waterway surface area of 0.6 km2, a catchment area of 6 km2 and a maximum depth

of ~ 3.5 m when closed, ~ 2 m when open. The frequency of opening events is high (2-3

times per year) and the opening duration is short, lasting approximately 1-2 weeks. The

majority of opening events are artificial; to mitigate flooding, and a channel is initiated

through the beach berm when internal water levels reach approximately 2.36 m measured

against the Australian Height Datum (AHD). During the breakout, approximately 700 mega

litres of water flows through the entrance in ~ 3 hours and peak average velocities reach

approximately 2 m s-1 (HR Wallingford 1994). During the breakout the channel width can

reach ~ 55 m and the maximum depth is ~ -1.0 m AHD (HR Wallingford 1994). The lake is

mainly shallow (< 1 m AHD) with a deeper region (~ 2 m AHD) existing closer to the inlet

and beach berm.


Figure 3.1 i) Map of Eastern Australia highlighting the location of the two field sites, ii)

Wamberal Lagoon, and iii) Smiths Lake. For both field sites the inlet can be seen to the east

and southeast of the water body, respectively, and is represented by a shaded region

connecting the ICOLL to the ocean. The symbol, X, marks the location of the deployed

instruments (ADCP and a CTD at depth and a CTD at the surface). The dots (●) represent

CTD profiles.


Smiths Lake (Figure 3.1) is located approximately 280 km north of Sydney, Australia and

has a waterway surface area of 11 km 2, a catchment area of 32 km 2 and a maximum depth of

5m (2.1m AHD) when closed. The frequency of opening events is low (once every 18

months) and the open duration is approximately 2-3 months. When open the maximum

depth is approximately 3.5 m (Webb et al. 1998). The majority of the opening events are

artificial, to mitigate flooding of nearby properties, and are induced when internal water levels

reach 1.7 - 2.1 m AHD. During the breakout, approximately 10,800 mega liters of water

flows through the entrance in 36 hours and peak average velocities reach 2.5 m s-1 (Webb et

al. 1998). The maximum-recorded width of the entrance is ~ 60 m, and the depth is

approximately -1.0 m AHD (Webb et al. 1998).

3.3 Methods

3.3.1 Field Observations

During the inlet-closed state, two CTD-DO loggers (Greenspan model CS305),

measuring conductivity, temperature, pressure and dissolved oxygen, were deployed (in

series) in the deeper region of each ICOLL (Figures 3.1). The CTD’s took measurements

every 30 minutes with a 5 minute averaging of the data. The data obtained from Smiths Lake

covered intermittent periods over 7 months and the data obtained from Wamberal lagoon

covered intermittent periods over 3 months over the years 2002-2003. This covered both the

closed and the open state within each ICOLL. Coinciding with the CTD measurements,

spatial profiles of salinity, temperature and dissolved oxygen were obtained at 0.5m depth

intervals throughout each ICOLL at 10 stations in Smiths Lake and 6 stations in Wamberal

Lagoon. During the open state, an ADCP (Nortek 2MHz Aquadopp), measuring water

velocities, was deployed alongside the CTD at the lakebed. The ADCP measured velocities


every 5 minutes, with an averaging over 1 minute, at 0.2m intervals in the vertical. Water

levels inside and outside the inlets and meteorological data were obtained from the Manly

Hydraulics Laboratory and the Bureau of Meteorology respectively.

3.3.2 Analysis methods

The potential energy anomaly method which has been successfully applied to estuaries

(Nunes et al. 1989; Ranasinghe & Pattiaratchi 1999) and more commonly to coastal seas

(Rippeth & Simpson 1996; Lund-Hansen et al. 1996) was used in this study to investigate

physical processes governing vertical mixing/stratification. The potential energy anomaly, �,

defines the amount of energy per unit volume required to stratify a mixed water column

(Simpson et al. 1990). The potential energy anomaly (�, J m-3) of the water column can be

defined as:

( )zdzHg

H∫

−

−=Φ0

ρρ (3.1)

where: ∫−

=0

)(1

h

dzzh

ρρ (3.2)

where, g is the acceleration due to gravity (m s -2), ρ is the water density (kg m-3), h is the water

depth (m) and z is the depth interval (m).

During the closed state, the vertical structure of the ICOLL is determined by a balance

between the stratifying influences of solar heating and rainfall, competing against the mixing

potential of wind and evaporative cooling. The terms forming the potential energy anomaly

equation can be grouped together to produce a value for potential energy changing over time

(dФ/dt):


paS C

gLEsEgh

WksPgCpQg

dtd

2222

3 αρβρδρβα−−−+=

Φ & (3.3)

(1) (2) (3) (4) (5)

where h = mean water column depth (m), δ = wind mixing efficiency, W = mean wind

speed (ms-1), sk = drag coefficient for surface stresses, aρ = density of air (kg m-3), β =

coefficient of saline contraction, s = salinity, E = rate of evaporation (m), α = thermal

expansion coefficient, L = Latent heat of transformation (from water to vapour) (Wm-2),

pc = specific heat capacity at standard pressure, Q& = net heating rate (Wm-2), incorporating

heating during the day and cooling at night, P = total precipitation (mm).

The bulk parameters required to calculate equation 3.3 are defined using a daily temporal

scale. Terms 1 and 2 represent the processes that introduce potential energy into the system,

and promote a stabilizing effect on the water column. Term 1 Hdt

d⎟⎠⎞

⎜⎝⎛ Φ represents the energy

received from surface heating from the sun; Term 2 Rdt

d⎟⎠⎞

⎜⎝⎛ Φ represents the energy received

from rainfall and is assumed to fall uniformly over the water body. Terms 3-5 represent the

processes that promote vertical mixing. Term 3 Wdt

d⎟⎠⎞

⎜⎝⎛ Φ represents the mixing energy

received from the wind and terms 4 and 5, collectively Edt

d⎟⎠⎞

⎜⎝⎛ Φ represent the negative

buoyancy flux of increasing surface salinity and latent heat loss due to evaporation (For a

more detailed explanation of the terms and their derivations please see Simpson et al. (1990)).

When the change in potential energy over time (dФ/dt) is positive, the water column


becomes stable and stratified, and when (dФ/dt) is negative the water column becomes

vertically well mixed or remains well mixed.

During the open state, an ICOLL experiences tidal forcing and exchange, and the

potential energy anomaly needs to be re-defined to accommodate for the potentially relevant

processes. The longitudinal density gradient between the ICOLL and the ocean drives a

gravitational circulation, promoting stratification of the water column. Whilst on a shorter

temporal scale the process of Strain Induced Periodic Stratification (SIPS), which occurs

during the neap tides, when the tidal amplitudes are smaller, produces a decrease in mixing.

The decrease in mixing energy reduces the ability of the turbulence to mix the whole water

column and the associated tidal straining, between the surface and bottom waters, on the ebb

flow, can promote a two layered flow. Upon the return flood tide, processes reverse and the

water column becomes well mixed again (Simpson et al. 1990). This is typical of systems

where the influence of freshwater is relatively weak and tidal mixing can usually easily

overcome any temporary stratification that may form. These stratifying processes

compete against mixing from the wind and tidal effects. During the open state the

processes promoting the set-up and breakdown of stratification can occur on an hourly

timescale; therefore the terms and temporal scale of the equation have changed, and the

energy received from solar heating is assumed to be a constant background value, at this

finer scale of resolution. The additional terms have been taken from Simpson et al.

(1990), and include gravitational circulation (1), tidal straining (2) and tidal mixing (4).

The equation changes to the following:

hWk

huksPg

dxdugh

dxd

Khg

dtd

SSDZ

33242

34

2ˆ031.0

3201 ρδρε

πρβρρ

ρ−−+⎟

⎠⎞

⎜⎝⎛+⎟

⎠⎞

⎜⎝⎛=

Φ (3.4)

(1) (2) (3) (4) (5)


where ε = efficiency of tidal mixing, dk = drag coefficient for bottom stresses, u =

mean amplitude of the tidal current (m), ZK = vertical eddy viscosity (m2s-1) and u =

depth mean current.

Term 1 Bdt

d⎟⎠⎞

⎜⎝⎛ Φ represents the gravitational circulation and Term 2

Tsdtd

⎟⎠⎞

⎜⎝⎛ Φ represents

the energy received from tidal straining, Term 3 represents the input from rainfall, Term 4

Tdtd

⎟⎠⎞

⎜⎝⎛ Φ and Term 5

Wdtd

⎟⎠⎞

⎜⎝⎛ Φ represents wind mixing. The equation follows the same

theory as equation 3.3, when the change in potential energy over time ⎟⎠⎞

⎜⎝⎛ Φ

dtd is positive,

the water column becomes stable and stratified, and when ⎟⎠⎞

⎜⎝⎛ Φ

dtd is negative the water

column becomes vertically well mixed or remains well mixed.

3.4 Results and Discussion

3.4.1 Closed state: summer conditions

Both field sites were sampled, during the closed state, in the late spring and summer

months of November to January 2003. The heat fluxes were calculated using bulk formulae

by Friehe and Schmitt (1976) and the daytime solar heating rate was 350 W m-2 and the

nighttime cooling rate was 200 W m-2, resulting in a positive net heating rate for both field

sites. The mean daily evaporation rate was 3.5 mm day-1.

At Wamberal Lagoon, during the week of field observations (28th November – 4th

December, 2002), the mean salinity of the lagoon was 23 and the water levels were 1.0m

AHD. The magnitudes of the terms in equation (3) were estimated from 7 days of field data

(Table 1). The input from net solar heating (dФ/dt)H was high (Table 3.1); however the ability

of the wind (dФ/dt)W to mix the shallow water column was the most significant process for


the majority of the time, and maintained a well mixed water body. A rainfall event of 18 mm

occurred on the 29th Nov, and caused a small increase in water level (0.02 m) and a peak in

the rainfall term (dФ/dt)R. On the 30th Nov the wind peaked in magnitude and the lagoon was

again dominated by vertical mixing. On the second last day of the record (3rd Dec), weak

stratification developed due to a drop in the wind magnitude, below 4 m s-1, whilst the mixing

energy derived from evaporative cooling (dФ/dt)E was a magnitude smaller than all the other

terms.

The local climate at Smiths Lake, exhibited a diurnal sea breeze with wind speeds in the

range 0 – 6 m s-1 (mean speed of 3 m s-1) and no rainfall. From the 4th – 9th January 2003, the

mean salinity of the lake was 28, and the lake water level was 1.1m AHD. The magnitudes of

the terms in equation (3) were estimated from 6 days of field data (Table 1). The net heating

rate was positive, indicating no overturning was occurring at night. The heating term

(dФ/dt)H was also the most significant process indicating that stratification was dominating

the vertical water column within the Lake (Table 3.1). Meanwhile the wind mixing (dФ/dt)W

and the mixing derived from evaporative cooling (dФ/dt)E, together, were not strong enough

to break down the vertical stratification. In order to promote a shift towards a vertically well

mixed system, the wind mixing (dФ/dt)W would need to increase to a daily mean value of 5 m

s-1 or greater. An examination of the local wind data for the summer months of 2002 – 2003

(not shown here) illustrated that peak wind speeds up to 7 m s-1 were common, and appeared

to be associated with the sea breeze. The winds never lasted for longer than half a day

though producing daily mean values of less than 5 m s-1 allowing thermal stratification to

persist.


Wamberal Lagoon

(J m-3 s-1) Smiths Lake

(J m-3 s-1)

Heating Term Hdt

d⎥⎦⎤

⎢⎣⎡ Φ 7 x 10 -5 1 x 10 -4

Precipitation Term Rdt

d⎥⎦⎤

⎢⎣⎡ Φ 4 x 10 -5 0

Wind mixing Term Wdt

d⎥⎦⎤

⎢⎣⎡ Φ 1 – 4 x 10 -4 7 x 10 -6

Evaporation Term Edt

d⎥⎦⎤

⎢⎣⎡ Φ 6 x 10-6 6 x 10-6

Table 3-1 The magnitude of the terms in equation (3.3) for Wamberal Lagoon and Smiths Lake under closed conditions (Note: Wamberal Lagoon and Smiths Lake data cover a period of 7 and 6 days respectively).

3.4.2 Closed state: predicting the winter conditions

The above analysis can be extended to examine closed-state mixing characteristics during

winter conditions using available meteorological data. The net heating and cooling rates were

lower at 200 W m-2, and 100 W m-2 respectively, but the solar heating was still greater than

the cooling, implying a positive net heating rate and an absence of overturning at night. The

energy received from net heating (stabilising term) was reduced to 4 x 10-5 J m-3 s-1, and the

evaporation rates also decreased to ~ 1.5 mm day-1 (mixing term, 1 x 10-6 J m-3 s-1)

The only changing variable between the two sites was wind, and it is also the only term

dependent on depth. If we assume there was no input from rainfall then the critical wind

speed for vertical mixing to be initiated in each ICOLL, can be calculated using the following

balance:

WEH dtd

dtd

dtd

⎥⎦⎤

⎢⎣⎡ Φ

+⎥⎦⎤

⎢⎣⎡ Φ

⎥⎦⎤

⎢⎣⎡ Φ ~ (3.5)


Assuming a mean salinity of 20, a mean temperature of 17oC, and (a) a mean depth of 1-2

m, the critical wind speed must be greater than 2 m s-1, and (b) a mean depth of 4 m, the

critical wind speed must be greater than 2.5 m s-1, to breakdown the thermally driven

stratification. The balance becomes more complicated when there is rainfall. The

occurrence of significant rainfall events may promote and/or enhance stratification, by

contributing to the buoyancy flux. Under both of the scenarios presented above a rainfall

event of 5 mm day-1 or greater would promote stratification, however if this is also coupled

with an increase in wind, as is often the case, then both terms will increase accordingly and

the ICOLL will become stratified or well mixed depending on each specific storm event.

3.4.3 Open State: autumn

The entrance channels at both field sites were artificially opened in May 2003. Immediately

after the opening of the inlet channel, the outflow dominated exchange in Wamberal Lagoon,

for the first 3 hours, whilst outflow dominated the exchange in Smiths Lake for 24 hours,

with the internal water levels of both ICOLLs dropping ~1.5 m, corresponding to the height

of the beach berm at the time of opening. In both systems the density was strongly

correlated to salinity (r2 = 0.99).

Wamberal Lagoon remained open for two weeks (Figure 3.2) and half way through the

opening event; the ICOLL was vertically well mixed. The energy in the individual forcing

terms from equation 4 indicated that the wind mixing and the tides (2 x 10-5 J m-3 s-1) were the

dominant process governing vertical mixing from the 21st to the 25th May (Figure 3.3). Tidal

straining was also of a comparable magnitude, and all other terms were negligible.

The water column velocities on the 22nd to the 25th May illustrated a decreasing input

from tidal forcing, as the tidal signal shifted from spring to neap. During this transition to

neap tides, there were two short stratification events on the 24th and 25th May (Figure 3.3).


During the first two tidal cycles (21st, 22nd May), there was a uniform inflow on the flood at

locations (a) and (b), in Figure 3.4(ii), however the tidal energy then decreased at locations (c)

and (d) (Figure 3.4(ii)) and the water column became temporarily vertically stratified. The

stratification events lasted ~ 5 hours and encompassed part of the flood tide as well as the

ebb tide. This may be due to a combination of the inlet beginning to close (complete closure

occurred on the 28th may) slowly reducing the degree of tidal mixing (u3) at the bed (Figure

3.4), low wind conditions and the process of tidal straining, which showed a peak in

Figure3.3 (iii).

Figure 3.2 Time series of (i) rainfall; (ii) water levels in Australian Height Datum (AHD);

and, (iii) wind data for Wamberal Lagoon for the months of May and June 2003 during the

open-state.

On the 26th May, Wamberal Lagoon experienced a period of stratification, which spanned

an ebb-flood-ebb, suggesting that a different mechanism, as opposed to SIPS, was driving


and/or stabilizing the stratification. The corresponding tidal velocities (Figure 3.4) showed a

lack of inflow at depth leading up to the event, which may have been partly attributed to the

neap tides, but may also have been partly attributed to the changing morphology of the inlet

channel. Surveys of the channel provided evidence that the entrance closed on the 28th May,

two days after the stratification event, and therefore a reduction in tidal velocities leading up

to the closure is feasible. On the 26th May, during the period of stratification, the stablising

influence of gravitational circulation, aided by the freshwater input from recent rainfall, easily

over-rode the reduced mixing influence of tidal and wind mixing (Figure 3.3).


Figure 3.3 Time series of (i) offshore forcing tidal water level in Australian Height

Datum (AHD), (ii) density for Wamberal Lagoon, during the open state, (iii) Individual

energy contributions and (iv) summary of the mixing vs. stabilizing terms within Wamberal

Lagoon during the open-state.


Figure 3.4 (i) Horizontal water velocities (ii) Energy derived from u3 and (iii) velocity

profiles during the prospective flood tides at Wamberal lagoon during open-state. Positive

velocities are directed into the lagoon and negative velocities are directed out of the lagoon.

The letters (a) through to (d) indicate the energy peaks derived from the flood tides and (iii)

are the corresponding vertical velocity profiles.

Smiths Lake remained open for 4 months (Figure 3.5). Immediately after opening, the

density gradient was strong (dρ/dx = 0.002 kg m-3) due to the relatively short longitudinal

length scale of the lake (5000 m). During this initial open period, the energy associated with

the forcing terms indicated that gravitational circulation (2 - 4 x 10-4 J m-3 s-1) dominated the

balance, whilst the remaining forcing terms (wind mixing, tidal mixing, tidal straining, rainfall

and net heating) were an order of magnitude smaller (10-5).

Two months into the opening (17th July) Smiths Lake remained stratified (Figure 3.6).

The longitudinal density gradient had weakened (dρ/dx = 0.0002 kg m-3), but the energy


associated with the forcing terms indicated that gravitational circulation was still a significant

process governing stratification, aided by tidal straining (1 - 2.5 x 10-5 J m-3 s-1). The wind was

also of a comparable magnitude and peaked at 6.1 m s-1, but did not manage to breakdown

the weak stratification, whilst the tidal velocities (< 0.1 m s-1) were also not sufficiently strong

to promote complete vertical mixing producing a negligible tidal mixing term (10-7). The net

heating and rainfall terms were also negligible (10-7) at this scale.

Figure 3.5 Time series of Meteorological data for Smiths Lake, including: (i) Rainfall; (ii)

Water level in Australian Height Datum (AHD); and (iii) Wind speed for the months of May,

June, July, August and September 2003, during the open-state.


Figure 3.6 Time series of (i) Offshore forcing tidal data, (ii) Density profiles of surface

and bottom waters within Smiths Lake, (iii) Individual forcing terms and (iv) Summary of the

mixing vs. stabilizing terms within Smiths Lake during the open-state.

Assuming a relatively steady forcing from the gravitational circulation, tidal straining, tidal

mixing and net heating, a sustained wind speed of ~ 7.5 m s-1 would be required to vertically

mix the lake. Local meteorological data (not shown here) illustrated that wind speeds


exceeded 7.5 m s-1 approximately 12 times in the years 2002-2004, again with no seasonal

preference.

3.4.4. Dissolved oxygen concentrations

The dissolved oxygen levels, within an aquatic system, represent a balance between

transport and mixing processes and biochemical constituents responsible for its utilization

(Herzfeld et al. 2001). In shallow basins, the dynamics of oxygen are likely to be dominated

by the physical processes of vertical mixing from the surface and sediment oxygen demand at

depth (Hearn and Robson 2001). During periods of stratification, when vertical mixing is

inhibited, depletion of oxygen in the bottom waters is expected through the consumption of

oxygen by the sediments. This has been observed in many estuarine systems including the

Harvey estuary, Australia (Hearn and Robson 2001), and the Neuse River, U.S.A (Borsuk et

al 2001). Under persistent stratification, the depletion of oxygen may lead to anoxia,

promoting stress within aquatic organisms and lead to associated changes in sediment redox

potential which can promote nutrient release (Kurup et al. 1998).

In the open state, Wamberal Lagoon experienced short periods of stratification

ranging from hours to approximately one day in duration. During the stratification phase

from 26th to 27th May, a linear regression was applied to the bottom oxygen concentrations

and showed oxygen a rate of decrease of 3.09 mg L-1 day-1.

The Buoyancy Frequency (N) can be used to estimate the strength of the density

gradient, where N is the frequency of the oscillation that develops when the pycnocline is

displaced, then left to return to its rest position (Mann and Lazier 1996). For N > 0, a

gravitationally stable condition exists, with density increasing with depth (Rubin and

Atkinson 2001):


⎟⎠⎞

⎜⎝⎛

⎟⎟⎠

⎞⎜⎜⎝

⎛=

dzdgN ρ

ρ (3.6)

In Wamberal Lagoon, it was found that the system stratified for N > 0.1 s-1, and

dissolved oxygen decreased after a short lag (Figure 3.7). The lag ranged between 5 – 10

hours for the three events, and may have been due to variations in sediment oxygen demand

or biological responses. During the third event, the surface waters showed an increase in

dissolved oxygen, which may have been due to the inflow of fresher water from the rainfall

event on the 25th May.

Whilst the onset of stratification produced a decrease of dissolved oxygen

concentrations at depth, research by Lucas et al. (1998) indicated that periodic stratification

does not necessarily promote poor water quality and increase the likelihood of a

phytoplankton bloom over that of an unstratified water column. Data from the present

study suggested that once the system mixed (either due to wind or tidal mixing) the oxygen

concentrations at depth were replenished from the surface waters and the probability of

anoxia was quite low. Assuming the observed rate of decrease of dissolved oxygen of 3.09

mg L-1 day-1, the stratification would need to persist at the observed strength for a period of

at least 2.5 days to promote anoxia of the bottom waters in Wamberal Lagoon. Along the

south east coast of Australia there can be long spells of rainy days, alternating with equally

lengthy periods of fine days (Gentilli 1972), suggesting that a rainfall event may promote

anoxia, if given the right conditions.


Figure 3.7 Time series of (i) Density for surface (____) and bottom (-.-.-.) waters, (ii)

Dissolved oxygen for surface (___) and bottom (-.-.-.) waters, and (iii) the Brunt -Vaisala

Frequency at Wamberal lagoon during open-state.

In the closed state, Wamberal Lagoon also experienced periods of decreasing

dissolved oxygen, under vertical stratification (not shown here). A period of weak

stratification occurred from the 2nd to the 4th December 2002; however the dissolved oxygen

concentrations did not experience a decline during this period, but continued to fluctuate

diurnally between 4.5 – 8 mg L-1. The Buoyancy Frequency (N) could not be calculated for

this event, due to intermittent conductivity data capture, but it is more likely that the diurnal

response of dissolved oxygen was due to biological processes such as photosynthesis and

respiration, (Gonenc and Wolflin 2005), than any significant changes in vertical mixing.

Immediately upon opening Smiths Lake, the reduction in vertical mixing, associated

with the strong longitudinal density gradient between the lake and the ocean, initiated a


decrease in bottom dissolved oxygen concentrations to ~ 5 mg L-1, by the 5th day. Two

months after the opening, Smiths Lake remained stratified and observations of the dissolved

oxygen concentrations showed a cyclic increase and decrease, on a diurnal and a fortnightly

cycle (Figure 3.8). The fortnightly variations in the field data suggest that it may be linked to

tidal influences.

In a study of shallow estuaries, Hinwood et al. (2005) found that the action of spring tidal

pumping can give rise to a net upstream advection of water over the neap-spring half-cycle

and a net downstream advection of water over the spring-neap half-cycle. This process is

different to the more common process of tidal pumping in which net upstream or

downstream transport of salt, due to dispersion, results from the non-zero correlation of tidal

discharge and salinity (Hinwood et al. 2005). The results from Smiths Lake showed a similar

pattern, as suggested by the process of spring tidal pumping, where there was a rise in water

levels over the neap-spring half-cycle (24th July – 5th August, Figure 3.8.) and a decrease in

water levels over the spring-neap half-cycle (6th – 12th August, Figure 3.8.). During the

spring-neap half cycle (18th – 24th July, Figure 3.8), a strong surface outflow was also

observed, driven by barotropic forcing and winds from the west. The presence of the sill (~

1.0 m depth) and low lake water levels may have restricted inflow at depth, leading to a net

advection of water out of the lake. During this time, there was no significant change in the

strength of the stratification (Buoyancy Frequency, N = 0.05 - 0.07 s-1), with both layers

decreasing in salinity at a similar temporal rate. The decrease in salinity of the bottom layer

was consistent with the vertical diffusion processes described by Mann and Lazier (1996).

Therefore the slight changes in the bottom dissolved oxygen concentration, during the neap

tides (21st – 24th July, Figure 3.8.), did not appear to be due to the strength of the

stratification, rather it was linked to the reduction in water level reducing the two layered

circulation with the ocean It was found that soon after the lake opened and the ocean water

initially started to penetrate into the lake, the dissolved oxygen decreased in the bottom layer,


rather than increased. However after the lake had been open for a couple of months, the

dissolved oxygen levels did appear to increase with increased seawater inflow at depth (Figure

3.8). It is thought that the sediment oxygen demand may play a role here, or maybe the sharp

change in salinity immediately after the lake opened has some biological response and

consequent consumption of dissolved oxygen at depth, but this was not investigated. As the

lake shifted towards the spring-neap half cycle, the direction of net advection was reversed

and directed upstream, leading to an increase in water level in the lake, penetration of oceanic

waters into the bottom layers and consequently, increases in bottom dissolved oxygen

concentration. Throughout this process the probability of anoxia appears relatively low.

In the closed state, field data (not shown here) from January 2003, suggested that

the dissolved oxygen concentration followed a diurnal trend, under weak stratification,

presumably due to biological processes such as photosynthesis and respiration. During this

time the dissolved oxygen levels remained above 7 mg L-1 thus the threat of anoxia would

appear relatively low, in the closed state too.

Previous research on intermittently opening lagoon systems has highlighted the

differences in ecological variables, between open and closed state in a single ICOLL and

across a suite of ICOLLs (Dye and Barros 2005, Pollard 1994). This study has demonstrated

that the processes controlling the vertical mixing can be different in the closed and the open

state, and may also vary between and within ICOLLs located in a similar climate. In the

closed state, thermal heating through solar insolation was often balanced by wind mixing, and

as the depth increased the effects of wind mixing were reduced and the ICOLL shifted from

a well mixed to a vertically stratified system. In the open state, tidal straining and

gravitational circulation were balanced by wind mixing, and as the water depth increased, the

strength of gravitational circulation increased, tidal straining also increased and the effects of

wind mixing were reduced, promoting a shift from a mixed to a stratified water column.


Figure 3.8 Smiths Lake data during the open state (i) Offshore tidal levels in Australian

Height Datum (AHD), (ii) Dissolved oxygen for the surface layer (darker line) and bottom

layer in Smiths Lake, and (iii) water levels for Smiths Lake during open-state. The vertical

lines highlight the regions of neap tides and drops in dissolved oxygen.

These states did not persist indefinitely though. Under ideal meteorological conditions, an

ICOLL showed the ability to switch between vertically mixed to stratified and back again,

within a short timeframe (hours to days). Rainfall events were significant for the stabilisation

of the shallower systems and, combined with periods of low wind and decreased tidal mixing,

could promote stratification within hours. The shallower systems were also more dynamic,

in this respect. There was, however, little variation with season, suggesting that although an

opening event can occur at any stage throughout the year, the seasonal timing is not

necessarily critical in defining the dominant vertical mixing processes.


This research also established that during times of stratification, in an ICOLL, the

strength of stratification (as measured by the buoyancy frequency) was the significant

indicator for the variation in dissolved oxygen concentration. When the strength of the

stratification reached a critical threshold, (Buoyancy Frequency, N > 0.1 s-1), the dissolved

oxygen concentration started to decrease. The delicate balance between the specific

stabilising and destabilising processes determined the strength of the stratification. Thermally

induced stratification was generally not sufficiently strong to reach the threshold, whilst

salinity driven density gradients produced stronger stratification. The latter stratification

events were often short (hours to days) and driven by a combination of a decrease in tidal

mixing, low winds and/or periods of rainfall. There was however, a lag between the onset of

stratification and the decline in dissolved oxygen at depth, which may be attributed to

chemical or biological processes.

These measurements and analysis highlight the significance of rainfall events during

periods of calm wind, to vertical mixing and stratification regimes in shallow lake and lagoon

systems. As well as emphasizing the potentially detrimental effects stratification events can

have for the ecology of a lake or lagoon, through a decrease in dissolved oxygen

concentrations. The ability to define the stratification event and its duration may be critical

to the ecological health of the lagoon.

3.5 Concluding remarks

The main conclusions from this study have been summarised in Table 3.2, and include:

• No dominant process was found to control vertical stratification in either of the two

ICOLLs, resulting in fluctuating periods of mixing and stratification.

• In the closed state, the most significant process in the larger deeper ICOLL was solar

heating which promoted thermal stratification for the majority of the time, however

strong wind events showed the ability to fully mix the system. In contrast the most


significant process in the smaller, shallower ICOLL was wind mixing; promoting a

generally well-mixed system, however periods of low wind and solar heating

exhibited the ability to stratify the lagoon for short periods (days) at a time.

• In the open state, the larger, deeper ICOLL the most significant process was

gravitational circulation, which maintained vertical stratification for the majority of

the time. Whilst the most significant process in the smaller, shallower ICOLL was

wind and tidal mixing, however a combination of one or more of periods of low

winds, variations in tidal mixing and rainfall showed the ability to stratify the lagoon

for short periods (hours to days) at a time.

• The dissolved oxygen conditions were intricately tied to the strength of the

stratification. In the deeper, larger ICOLL the surface and bottom dissolved oxygen

concentration followed a diurnal trend and levels were maintained above ecological

guidelines (6 mg L-1 (ANZECC, 2000)). However, in the smaller, shallower ICOLL

the bottom dissolved oxygen concentration showed decreasing trends when the

strength of the stratification crossed a critical threshold, (Buoyancy Frequency, N >

0.1 s-1).

Dominant Status

Significant processes

Dissolved Oxygen Conditions

Wamberal Lagoon

Closed Mixed Wind Healthy Open Mixed Rainfall, low wind,

variations in tidal mixing

Decreases under strong stratification (N > 0.1 s -1)

Smiths Lake Closed Stratified Heating Healthy Open Stratified Baroclinic

circulation Healthy, but decreases

slightly around neap tides

Table 3.2 Summary of the two ICOLL states and implications for their dissolved oxygen concentrations


CHAPTER 4

PROCESSES DRIVING CIRCULATION, EXCHANGE AND FLUSHING

WITHIN INTERMITTENTLY CLOSING AND OPENING LAKES AND

LAGOONS

4.1 Abstract

The circulation and exchange between two Intermittently Closing and Opening Lakes

and Lagoons (ICOLLs), and the ocean, were analysed using salinity and current meter data.

Wamberal Lagoon was shallow (~ 2.5 m max depth) with a small (< 1km2) waterway area

and a short opening duration (2 weeks), and Smiths Lake was deeper (~ 5m max depth) with

a larger (~ 11km2) waterway area and a longer opening duration (4 months). An absence of

river inflow and a restricted sill type inlet channel characterized both systems. The results

demonstrated that although tidal effects controlled the circulation and exchange in the

smaller ICOLL, the wind also had a significant influence. In the larger ICOLL, in addition to

tidal and wind effects, sub tidal effects over the fortnightly tidal cycle also influenced the

circulation and exchange. An analysis of the flushing timescales illustrated that even though

the two ICOLLs experienced different exchange characteristics, the timescale of flushing was

comparable to the duration of opening, ranging from 4 days in the smaller ICOLL

(Wamberal Lagoon) to 113 days in the larger ICOLL (Smiths Lake).

4.2 Introduction

Coastal lakes and lagoons occupy 13% of the world’s coastal areas (Kjerfve 1994),

and Intermittently Closing and Opening Lakes and Lagoons (ICOLLs) are an important sub

category, due to their limited exchange with the ocean and their lack of river inflow. The


limited exchange is influenced by a restricted shallow inlet that is only open for intermittent

periods (weeks to months) throughout the year. The ICOLL water levels are driven by

rainfall and runoff alone, and when the levels become super elevated the ICOLL is opened to

the ocean, either naturally or artificially. During the closed state, an ICOLL is particularly

vulnerable to the trapping of nutrients and contaminants (Roy et al. 2001) and due to the

intermittent and variable opening period, lagoon systems are often poorly flushed (Kjerfve

and Magill 1989). In addition, the occurrence of high nutrient loads in these shallow, well lit

systems favour the development of substantial biomass of attached and floating macro algae

(Collett et al. 1981) and one consequence is the practice of artificially opening the lakes to

increase flushing and enhance water quality (Dye and Barros 2004).

When the ICOLL is open to the ocean, the inlet channel restricts exchange and is

itself subject to gradual change due to longshore and cross shore processes transporting sand

into the inlet. Sudden restriction may also occur due to onshore sediment movement

associated with large storm events (McLean and Hinwood 1999). In shallow systems

estuarine circulation is generally restricted by the shallow depth (Dyer 1997) and the

circulation within the water body can be highly responsive to wind forcing, because of their

characteristically large surface area to depth ratio (Smith 2001). Existing literature has

identified that in weakly forced tidal systems, low frequency water level oscillations are often

more effective in exchanging waters with the ocean than the tidal currents (Holloway 1996,

Janzen and Wong 1996). A specific low frequency process operating at a fortnightly timescale

is the action of Spring Tidal Pumping (STP) (Hinwood et al. 2005), which is the increase in

mean water level of a lake or lagoon due to spring tides. STP may occur in shallow lakes and

lagoons where the inlet cross sectional area varies significantly with depth. The difference in

channel depth, between the flood and the ebb tide, means that the ebb current flows through

a smaller cross section and encounters relatively higher resistance (Hinwood et al. 2005). This

process raisers the mean lake or lagoon water level. As the ratio of the ocean water level (tide)


to the channel depth increases so does the mean water level within the lake / lagoon and this

promotes a fortnightly tide. Characteristics of the fortnightly tide may also change due to

sedimentation of the inlet or changes to the tidal forcing (Hinwood et al. 2005). Earlier work

by Hill (1994) and Dias et al. (2000) also identified a fortnightly variation in water levels in

lagoon systems, but did not give the term a name. All of these processes become critical

when the exchange time with the ocean is limited.

Along the southeast coastline of Australia there are over 135 estuaries of which 45%

are intermittently open (Pollard 1994). Within the sub category approximately 72% are

artificially opened (DNR 2004). The frequency and duration of the opening event can vary

between and within ICOLLs, with frequencies ranging from 2-3 times per year, to once every

2 years, and the duration can vary from weeks to months.

The restricted inlet and large variability in opening frequency and duration suggests

that the dynamics of exchange and flushing, during the limited opening time, may be quite

important for the water quality of the ICOLL through the transport of nutrients and

pollutants, as well as the ecology, through the regulation of salinity. The aim of this study was

to examine, in detail, the circulation, exchange and flushing characteristics of two

intermittently closing and opening lake and lagoon systems. The two systems were chosen as

representative end members of the suite of ICOLLs found along the south east coast of

Australia, with the first ICOLL, Wamberal Lagoon, representing one of the smaller lagoon

systems, which experiences a short opening duration (weeks), whilst the second field site,

Smiths Lake, represents one of the larger lake systems which experiences a longer opening

duration (months). The results will then examine any differences in exchange and flushing

between the two ICOLL systems.


4.3 Materials and methods

4.3.1 Field site descriptions

The first field site, Wamberal Lagoon (Figure 4.1), is artificially opened 2 -3 times per

year, but only maintains the open state for 1-2 weeks. The second field site, Smiths Lake is

artificially opened less frequently (once every 18 months) and maintains an open state for

between 1 - 4 months of the year. The two systems are similar in most other aspects,

including climate and morphology. The regional climate is temperate with an average annual

rainfall greater than 800 mm with no marked seasonality. The ocean tides are mixed, mainly

semi-diurnal (form number = 0.54) and micro-tidal (< 2 m) in nature. The predominant

winds are southerly (summer) and westerly (winter) (Gentilli 1972). Strong onshore sea

breezes also occur in summer (Gentilli 1972).

The smaller ICOLL, Wamberal Lagoon (Figure 4.1b) is located approximately 90 km

north of Sydney and has a waterway surface area of 0.6 km2, a catchment area of 6 km2 and a

maximum depth of ~2.5 m when closed. The majority of opening events are artificial; to

mitigate flooding and a channel is initiated through the beach berm when lagoon water levels

reach approximately 2.4 m Australian Height Datum (AHD). During the breakout,

approximately 400 Mega Litres (ML) of water flows through the entrance in the first 3 hours

and peak average velocities reach approximately 2 ms-1 (HR Wallingford 1994). During the

breakout the channel width can reach approximately 55 m and the maximum depth reaches

approximately -1.0 m AHD (HR Wallingford 1994). The inlet channel is orientated southeast

– northwest and the majority of the lake is quite shallow (< 1 m) with the deeper region (~ 3

m) existing closer to the inlet channel.

The larger ICOLL, Smiths Lake (Figure 4.1c) is located approximately 280 km north

of Sydney and has a waterway surface area of 11 km 2, a catchment area of 32 km 2 and a

maximum depth of ~5 m when closed. The majority of the opening events are artificial, to


mitigate flooding of nearby properties and occurs when lake water levels reach 2.1 m AHD.

During the breakout, approximately 10 800 Mega Litres (ML) of water flows through the

entrance in 36 hours and peak average velocities reach 2.5 ms -1 (Webb, McKeown and

Associates 1998). The maximum recorded width of the entrance is ~ 60 m wide, and the

depth is approximately -1.0 m AHD (Webb, McKeown and Associates 1998). The inlet

channel is orientated east – west, with a large shallow region existing between the tidal inlet

channel and the main body of the lake (Figure 4.1c).

4.3.2 Data collection

Wamberal Lagoon was artificially opened on the 14th May 2003, and remained open

for two weeks. During this time, the following instruments obtained the collection of field

data. A Nortek Acoustic Doppler Current Profiler (ADCP) was deployed at the bed, near the

inlet channel (Figure 4.1b). The ADCP had an acoustic frequency of 1 MHz and measured

horizontal velocities every 10 minutes, with an averaging interval of 1 minute and a vertical

spacing of 0.2 m. The ADCP data covered the second week of a two-week opening event

(May 2003). Two Greenspan Conductivity, Temperature and Depth (CTD) probes were also

deployed at the same location, one at the bed and one at the surface, suspending by a buoy.

The CTD’s recorded information at 30 minutes intervals, with an averaging interval of 5

minutes. One spatial series of temperature and salinity profiles was obtained immediately

upon closure, using a Yeokal 611 Water Quality Analyser. The morphology of the inlet was

also mapped over the two-week opening event, at weekly intervals.


Figure 4.1 a) The east coast of Australia with a box highlighting the location of the two

field sites, (b) Wamberal Lagoon and (c) Smiths Lake. The inlet can be seen to the east, and

south east, respectively of each lake, and is represented by the shaded region connecting the

lake to the ocean. The symbol, X, marks the approximate locations of the deployed

instruments (ADCP at depth and a CTD at depth and at the surface) and the dots (●)

represent the approximate CTD profile locations.


Smiths Lake was artificially opened to the ocean on the 15th May 2003, and remained

open for approximately 4 months. A similar field set up, as for Wamberal Lagoon, was

deployed in this lake (Figure 4.1c). An ADCP was deployed at the bed, near the inlet channel

(Figure 4.1b) and measured horizontal velocities every 10 minutes, with an averaging interval

of 1 minute and a vertical spacing of 0.2 m. The ADCP data consists of 2 days immediately

following the opening event and 2 weeks in July 2003 (2 months after the opening event). At

the same time, two CTD probes were deployed at the same location, one at the bed and one

suspended near the surface, and recorded information at 30 minutes intervals, with an

averaging interval of 5 minutes. The data obtained from the CTD’s covered approximately

1.5 months (July – September 2003) with intermittent data over the remainder of the opening

period (May – July 2003). A Yeokal 611 water quality analyser was also used to collect vertical

profiles of temperature and salinity from 10 locations throughout the lake, in May and July

2003.

Water levels from within the two ICOLLs and observed offshore sea level heights

were obtained for the entire opening period from Manly Hydraulics Laboratory, NSW,

Australia, and corresponding meteorological data were obtained from the Bureau of

Meteorology, Australia.

4.3.3 Data Analysis

To determine the dominant circulation and exchange characteristics, salt fluxes have

been calculated for each field site. The method has been modified from Dyer (1997).

Immediately prior to an opening event, the ICOLL may contain predominantly fresh,

brackish or saline water, depending on the duration of closure from the ocean, the extent of

freshwater inputs and evaporation rates over this time. When open, the resulting flux of salt

between the ocean and the ICOLL becomes a valuable indicator of exchange, due to its


conservative nature. This method and similar variations have been successfully applied to the

Conwy estuary (Simpson et al. 2001), Willapa Bay (Banas et al. 2004) and the San Juan delta,

Colombia (Restrepo and Kjerfve 2002).

The total flux of salt, per unit width, through a vertical section can be averaged over a

tidal period to give the net flux, F, as calculated by:

( )dzusFh

∫=0

(4.1)

Where u(z) is the observed velocity and s(z) is the observed salinity, z is the vertical

coordinate and h is the depth. The flux is considered to be at a steady state, with the

advective and diffusive modes of transport balancing the exchange. The flux can be

decomposed into the following terms (Restrepo and Kjerfve 2002):

suhuhsshushusuhF TTTTTT ′′++++= (4.2)

(1) (2) (3) (4) (5)

uuu ′+= (4.3)

Tuuu += (4.4)

Where u is the observed velocity and is made up of a depth mean velocity component, u

and a turbulent velocity component, u′ (equation 4.3). The brackets represent a tidally

averaged (over a flood and ebb tide) term. In this case the data was averaged over two flood

ebb cycles to represent approximately one day. The mean velocity component,u , can be

further broken down (equation 4.4) into a tidally averaged velocity < u > and a tidally


varying (during the flood ebb cycle) velocity Tu (equation 4.4). The same theory is applied to

salinity (s).

The advective flux (term 1) is due to the mean tidal flow and is associated with the

change in storage during the tidal cycle, representing a net emptying or filling of the system.

Term 2 represents tidal pumping, and refers to the net transport of salt by oscillatory tidal

currents over a tidal cycle and is usually directed upstream. This flux usually reaches a

maximum when currents and salinity are in phase and is usually the major landward flux

component in well-mixed systems (Restrepo and Kjerfve 2002). Term 3 represents the cross

correlation between tide and salinity, which represents any time lag in change in salinity

associated with a change in water depth. Term 4 represents the Stokes drift dispersion, and

accounts for the dispersion of salt related to the net drift of water in the direction of wave

travel (Masselink and Hughes 2003). Term 5 represents the salt dispersion due to mean shear

produced by the presence of gravitational circulation.


4.4.1 Tidal and wind forcing in Wamberal Lagoon

Wamberal Lagoon was artificially opened on the 14th May 2003, and remained open

for two weeks. A harmonic analysis was undertaken on a subset of water levels, which were

extracted from the middle of the water level record, so as to reduce interference from a

changing inlet. The results identified the K1, M2, M3 and M4 as being the dominant tidal

constituents (Table 4.1). A comparison between the lagoon and the ocean showed that the

diurnal constituent K1 was reduced by 41% and the semi diurnal constituent M2 was reduced

by 55%. Within the lagoon the shallow water constituents, M3 and M4 were significantly


enhanced by at least one order of magnitude. The lower frequency constituents were not

defined due to the short opening time of the lagoon.

Table 4.1 Harmonic Analysis of the tidal constituents within Wamberal Lagoon, and the

Ocean

The tidal excursion was calculated by multiplying the inflowing mean velocity (~ 0.15

m s-1) by the duration of the flood tide (~ 4 hours) and this produced a tidal excursion of

approximately 1800 m, which was equivalent to the length scale of the lagoon. The Rossby

number, Ro, determines whether Coriolis forces are significant in the lagoon, and can be

calculated as follows:

fLURo = (4.5)

Where U = velocity scale, f = Coriolis parameter and L = horizontal length scale.

The Ro was calculated as ~1, which suggested that rotational effects may be important.

During 21st – 23rd May 2003, the wind climate was weak (< 5 m s-1) and was

dominated by westerly winds, orientated in the direction of outflow through the inlet. Inside

the lagoon a typical flood tide, during this period, was dominated by a uniform inflow of

Lagoon Ocean Lagoon Ocean

Tide Period (hr) Amplitude Amplitude Phase Phase

K1

23.93 0.112 0.188 204.51 141.7

M2

12.42 0.229 0.504 28.54 259.88

M3

8.27 0.039 0.002 143.54 46.16

M4

6.21 0.042 0.0004 350.28 197.08


water through depth (Figure 4.2a) and a typical ebb tide was represented by a dominant

surface outflow (Figure 4.2b).

Figure 4.2 Wamberal Lagoon mean velocity profiles (a) Typical flood tide, (b) Typical

ebb tide, (c) mean circulation, over 4 days, and (d) residual circulation during a rainfall event,

lasting 1.5 days (positive = flow into lagoon, negative = flow out of lagoon)

The residual circulation (Figure 4.2c) retained the dominant surface outflow, with a

maximum velocity of 0.1 m s-1, and negligible inflow at depth. From the 24th to the 27th May,

a storm front passed through the region, with predominant southerly winds > 5 m s-1. The

residual circulation for this period (Figure 4.2d) showed a reversal in the direction of the

surface current, resulting in a landward flow with a magnitude of ~ 0.2 m s-1 (also shown in

Figure 4.3d). This is most likely due to wind forcing at the surface, as the flow direction (to

the north-west) was similar to the dominant wind direction (to the north). In the middle of

the vertical profile the water was flowing in the opposite direction and the flow at depth was

negligible (Figure 4.2d). The lack of strong seaward flow suggests that exchange with the

ocean had been hindered, especially at depth, and this corresponds well with the recorded

closure of the inlet on the 28th May. The corresponding decrease in the mean salinity (Figure

4.3c) highlighted the input from rainfall (26th-27th) during the storm event; and Chapter 3


confirmed that stratification was produced during this time. This may have produced the

weak two-layered circulation, which was then driven by the wind, and influence by Coriolis.

Figure 4.3 Time series of (a) wind direction, (b) wind speed, (c) hourly averaged mean

salinity within Wamberal Lagoon, where the drops in salinity correspond to periods of

stratification (Chapter 3) and (d) surface and bottom velocity data, where a positive velocity is

flowing into the lagoon, a negative velocity is flowing out. This data was taken during the

second week of a two-week opening event. The region [A] contains the period of

predominantly southerly winds and large surface currents.

4.4.2 Oceanic exchange within Wamberal Lagoon

To define and quantify the processes dominating the exchange between Wamberal

Lagoon and the ocean, an analysis of the type of flow through the shallow inlet and

corresponding salt flux were undertaken.


The flow through the inlet may be largely affected by the inlet channel geometry.

Field surveys of the inlet provided evidence of slow infilling of the channel, with the initial

channel depth starting at -2.0 m AHD, decreasing to approximately -1.0 m AHD after one

week, and closing towards the end of the second week. The length of the inlet channel was

approximately 30 m. When turbulent mixing is thought to dominate flow through a channel,

as may be the case here due to the shallow nature of the inlet, then the degree of mixing can

be determined, by calculating the turbulent Grashof number, TGr multiplied by the aspect

ratio, A (Hogg et al. 2001) as follows:

2

2

32 '

⎟⎠⎞

⎜⎝⎛=

LH

KHgAGrv

T (4.6)

Where A is the aspect ratio H/L, H is the inlet channel depth, L is the length of the

channel, g’ is the reduced gravity given byo

gρ

ρΔ , and Kv =10-3 m2s-1 is the turbulent eddy

viscosity and is assumed to be constant. Recorded values for the 2AGrT range from 101 to

107 (Hogg et al. 2001) where the smaller the number, the greater vertical mixing that is

occurring.

From equation (4.6) the 2AGrT = ~ 101, using data from the 21st and 22nd May. This

value predicts that the velocity in the channel is limited by turbulent eddy viscosity and

transport of mass is due to a combination of advection and turbulent diffusion (Hogg et al.

2001). The interface thickness, ht, of the flow can then be calculated as follows (Hogg et al.

2001):

( ) 4/124.3 −= AGrh Tt (4.7)


For values where ht > 1, Hogg et al. (2001) predicts that mixing of the flow is 100%

of the flow through the channel. Therefore, in the case of Wamberal Lagoon (ht > 1) it was

highly likely that the flow through the channel was homogenous, and that there was no

baroclinic exchange occurring in the inlet with the flow being driven solely by barotropic

forcing.

To quantify the exchange through the channel, field data from the second week of

the opening (21st – 27th May) was utilised to calculate the salt flux. From the 22nd to the 25th

May, the exchange was directed out of the lagoon and the values ranged from 1 – 3 ppt cm s-

1 (Figure 4.4). The mean flow ( suh ) accounted for 86 – 96 % of the total exchange,

over the 4 days, and the remaining terms all accounted for < 10 % each.

On the second last day the trend was reversed, and the dominating mean flow

( suh ) was directed into the lagoon. During this time there was a storm event and the

lagoon experienced strong southerly winds, which appeared to dominate the surface flow

(section 4.4.1), this most likely caused the shift in the flux. The inlet had also begun to close

(section 4.4.1) suggesting that the large flux associated with the mean flow may not be

accurately assumed to be coming from the ocean, and may be due to re-circulation within the

lagoon. During the last day, the dispersion term, which is associated with gravitational

circulation, ( >′′< suh ) increased in magnitude. This was most likely due to the presence of

stratification (section 3.4.3). The values for the last 2 days of the record may however not

accurately portray the flux between the lagoon and the ocean due to the nearing closure of

the inlet allowing minimal exchange to occur. The tidal pumping term ( >< TT shu ) was not

a significant contributor to the flux on any of the days.


Figure 4.4 Wamberal Lagoon (a) Rainfall, (b) Sea Levels, (c) lagoon water levels, and (d)

Salt Flux (positive = flow into lagoon, negative = flow out of lagoon)

4.4.3 Tidal and wind forcing in Smiths Lake

Smiths Lake was artificially opened on the 15th May 2003 and remained open for

approximately four months. The main tidal constituents were defined by a harmonic analysis

(Table 4.2) of the lake water levels, which were extracted from the middle of the water level

record, so as to reduce interference from a changing inlet. The results illustrated a dampening

of the major tidal constituents within the lake. The K1, O1 and M2 were reduced by 83%,

66% and 93% respectively. Only one shallow water tide, M4, showed up, whilst two low

frequency tidal constituents were defined; the MM at a frequency of 30 days, with a similar

amplitude as the dampened K1, O1 and M2 (~ 0.03m), and the MSF with a at a frequency of

14.77 days, showed the largest amplitude at 0.06m.


Table 4.2 Harmonic Analysis of tidal constituents with Smiths Lake and the Ocean

During the first 24 hours after opening, the mean velocity profile (Figure 4.5a)

showed a strong outflow in the surface waters (0.4 m s-1) and an inflow (0.2 m s-1) at mid

depth (-2.0 m). The profile persisted until the morning of the 16th July 2003. The Rossby

number, Ro (equation 4.3) resulted in a value of ~ 0.25 indicating that rotational effects were

important in this lake. However, two months after the opening, the system exhibited no

significant horizontal variability in salinities within the lake (data not shown here).

Lake Ocean Lake Ocean

Tide Period (hr) Amplitude Amplitude Phase Phase

MM 661.31 0.032 0.015 233.7 30.26

MSF 354.37 0.066 0.021 317.32 63.18

O1 25.82 0.028 0.082 71.06 325.18

K1 23.93 0.031 0.178 12.53 284.14

N2 12.66 0.006 0.089 70.21 2.72

M2 12.42 0.028 0.410 16.41 285.53

L2 12.19 0.002 0.018 99.46 51.51

S2 12.00 0.005 0.070 308.33 190.89

M4 6.21 0.005 0.018 320.7 10.85


Figure 4.5 Smiths Lake velocity profiles (a) Tidal cycle initially after opening, (b) a typical

flood tide 2 months after opening, (c) a typical ebb tide 2 months after opening, and (d) the

mean circulation over a tidal cycle, 2 months after opening. Positive velocities indicate water

flowing into the lake, and negative velocities indicate water flowing out of the lake.

Over a 7 day period in the middle of July, the typical flood tide (Figure 4.5b) was

represented by an inflow at depth (~ 0.08 m s-1) and a surface current directed seaward (~

0.09 m s-1). On the ebb tide (Figure 4.5c), the flow reversed at depth (~ 0.1 m s-1) and was

directed seaward and the surface current also remained directed seaward, but increased in

velocity ( ~ 0.15 m s-1). The residual circulation (Figure 4.5d) showed a dominant surface

outflow (~ 0.08 m s-1), with negligible velocities at depth, exhibiting a net transport of water

out of the lake.


Figure 4.6 Wind responses within Smiths Lake on the 17th July, 2003. (a) Wind direction,

(b) wind speed, (c) offshore tidal signal, and (d) surface and bottom velocity data. A positive

velocity represents water flowing into the lake and a negative velocity represents water

flowing out of the lake. The region identified with the letter [A] represents the region of high

surface flows.

During periods of higher winds, the wind driven currents were stronger than the tidal

currents. On the 17th July 2003, the predominant winds were from the west and peaked

during the middle of the day at 3 m s-1. The corresponding surface currents (Figure 4.6)

reached 0.3 m s-1 and favoured the direction of outflow from the lake.

4.4.4 Low Frequency forcing within Smiths Lake

The harmonic analysis for Smiths Lake highlighted the low frequency tidal

constituents (Table 4.2) as potentially dominant processes driving water level fluctuations.


Therefore spectral analysis of the water levels (3.5 months of data) was undertaken, to

quantify the low frequency forcing within the lake. The beginning and end of the water level

record were removed due to potential interference from the changing inlet geometry. It

should be noted though, that changes in the inlet geometry may still be affecting the

following analysis. The analysis was also undertaken on the offshore tidal water levels, to gain

an understanding of local and remotely forced processes. The analysis confirmed the

dampening of the high frequency forcing (O1, K1 and M2) within the lake, whilst also re-

producing the peak in the low frequency band at 15 days. Whilst the low frequency peak at

15 days may be driven by the Msf tidal constituent, as highlighted in the harmonic analysis, it

may also be due to the action of tidal pumping or spring tidal pumping, all of which have a

similar frequency. The specific process producing this peak was investigated further. Smaller

peaks were also evident between 1 – 10 days (Figure 4.7), and can be attributed to

atmospheric forcing such as wind (Griffin and Middleton 1991). The area under each of the

peaks in the spectral analysis was calculated to provide an estimate of the energy

contribution, from each frequency, into the lake. The results showed that only 2 % of the

energy coming into the lake was from tidal forcing (cf. 96 % in the ocean) and approximately

87.5 % was derived from the lower frequency forcing as opposed to only 4 % in the ocean,

defining it as a much more significant process than the high frequency tidal forcing.


10

Figure 4.7 Spectral density plots of water level fluctuations within Smiths Lake (solid

line) and the ocean (dotted line) over a 6 week period in 2003.

A closer examination of the sub tidal lake water levels from the 17th July to the 10th

August 2003 (Figure 4.8) showed a fortnightly variation of approximately 0.5 m. This was

much greater than the combined amplitude of all the identified tidal constituents (0.2 m)

(table 4.2) and suggested that another source of sub tidal forcing may be present within the

lake.


Figure 4.8 Low pass filtered (25hrs) water levels for Smiths Lake, where asb = above sea

bed.

4.4.5 Oceanic exchange within Smiths Lake

There was no accurate mapping of the inlet channel, so the turbulent Grashof

number could not be calculated. Two months after the opening event, the salt flux was

calculated, for one week in July 2003 (16th – 22nd). The results showed that the exchange was

directed out of the system, varying slightly in magnitude, over the week (Figure 4.9). The

mean flow ( suh ) dominated the exchange, whilst all other terms were negligible,

including the tidal pumping term ( >< TT shu ). This confirmed that tidal pumping was not a

significant contributor to the salt flux, and the observed fortnightly variations were more

likely due to the process of Spring Tidal Pumping (STP). Two small rainfall events were

recorded on the 17th and the 19th July, and corresponded to a slightly smaller exchange.


Figure 4.9 Smiths Lake (a) Rainfall, (b) Sea level heights, (c) Lake water levels, and (d)

Salt flux derived from field data (positive = flux into lake, negative = flux out of lake)

To examine the influence of the spring tidal pumping, on the exchange, at a longer

timescale, a T-S diagram covering data from the 16th July – 10th August 2003, was plotted for

the surface and bottom waters (Figure 4.10). The surface water mass changed in salinity from

(1) to (2) (Figure 4.10) during the neap (21st) to spring (28th) tides, with a gradual increase in

salinity. During the following spring (28th) to neap (4th) tides, the water masses (2) and (3)

returned half way back to (1) and during the following neap (4th) to spring (11th) tides the

water composition changed very little. The variation in response within the lake, over the two

neap - spring cycles appeared to correspond to variations in the mixed, semi diurnal tidal

signal from the ocean.


Figure 4.10 (a) T-S plot of the surface and bottom waters within Smiths Lake, covering

data from the 16th July to the 10th August 2003. The water masses are identified by the

numbering (1) through to (4), and the surface waters are identified with an s, and the bottom

waters are identified with a b, (b) Sea level height for the corresponding period, including the

timing of the water masses identified by the numbering 1 through 4 above.

The first set of neap tides (~ 21st July) had a smaller diurnal inequality, when

compared to the second set of neap tides (~4th August), which suggested that the variations


in diurnal inequality, influenced by the proximity to the solstice, promoted variations between

the fortnightly cycles. The process of spring tidal pumping, however, was the dominant

process in exchanging waters with the ocean.

4.4.6 Flushing timescales for the two ICOLLs

To determine the flushing timescale for each ICOLL it was first required to define

whether the water being transported by the mean flow was predominantly new ocean water

or old lagoon water returning. The Tidal Exchange Ratio (TER), as described by Fischer et

al. (1979), calculates the ratio (R) of new water versus the total water entering the lake on the

flood tide and can be calculated as:

( )( )eo

ef

SSSS

R−

−= (4.8)

Where Sf = the average salinity of water entering the estuary on the flood tide, Se =

average salinity of water leaving the estuary on the ebb tide, and So = the salinity of the ocean

water. Some caution is needed when applying this method to systems that have variable

freshwater inflow, as the lagoon water reaches the salinity of the ocean, the TER reaches

zero, even though exchange of new waters may still be occurring.

Two days of data were analysed for Wamberal Lagoon and the results illustrated that

the mean flow was transporting 55% of ‘new’ ocean water into the lagoon on the 22nd May,

2003, and then 21% on the 23rd May. The input of freshwater from the rainfall event on the

26th May, increased the TER back up to 52 %.

In Smiths Lake, the TER was calculated for each day over the period 17thJuly – 10th

August. The results showed a large variation, corresponding to the timing of the spring neap


cycle (Figure 4.11), with the lowest TER, of 0.08, occurring during the neap tides (24th July),

and the highest TER, of 0.56, occurring during the spring tides (2nd August). There were no

rainfall events in Smiths Lake during this period.

To determine the flushing timescale ( fT ) for each lake, the bathymetry data, tidal

amplitude and TER were used to calculate the following (Dyer 1997):

PSS

SSVT

eo

meanof ε/⎟⎟

⎠

⎞⎜⎜⎝

⎛−

−= (4.9)

Where V = the low tide volume, P = the intertidal volume (tidal prism), Smean = mean salinity

of the water column and ε = fraction of ebb water not returning on the flood (which is the

inverse of R (equation 4.8). For Wamberal Lagoon, with a mean depth of -1.5m, and a TER

of 55 %, the flushing timescale was of the order of 3 - 4 days. A comparison of the flushing

timescale, with the exchange rate of 1-2ppt cm s-1 (as previously calculated) suggests that

complete flushing of the lagoon (1.2 x106 m3) in 4 days is not possible. This suggests that

there are most likely different exchange rates occurring at different times during the two

week opening and that a much faster exchange rate would have to be occurring at the

beginning of the opening. The differences in exchange rates may be influenced by the spring

neap cycle producing different tidal forcing, the inlet geometry or other local and remote

forcing. However, the field data (Figure 4.3c) obtained 8 days after the opening (21st May),

confirmed that the system was well mixed (salinity of 34 ppt) and that a fT = 4 days, using

the available data, was feasible.

For Smiths Lake, with a mean depth of –3m and a large variation in TER, the flushing

timescale was calculated for each day of the 25-day period (Figure 4.11c). The variation in

flushing timescale ranged from 39 - 370 days. If we assume that the greatest variations within

the TER results and the flushing timescales occurred during the spring neap cycle (15 day


frequency), then we can calculate a mean TER, for the 15-day period (19th July – 2nd August)

and use it as a representative value for the lake. This provides a mean TER of 0.23, which

then produces a flushing timescale of approximately 113 days. The timing of the field data,

captured 60 days after the opening, can only confirm that the lake was still not completely

flushed at this time, with mean lake salinities of 28 ppt.

Figure 4.11 Smiths Lake (a) Sea Level heights, (b) mean salinity, and (c) Tidal Exchange

Ratio (TER). Note the small TER around the time of neap tides (22nd July) and the rise in

TER around the period of spring tides (1st August), indicating periods of lesser and greater

exchange with the ocean.


The results from this research demonstrated that the two different ICOLLs exhibited

similar residual circulation patterns, dominated by a surface current directed out of the lake /

lagoon, but the origin of the surface waters was different. This varied from the typical

estuarine circulation pattern, where in a permanently open estuary; the surface outflow is

balanced by the inflow at depth, regardless of the origin of the surface waters. In the smaller


ICOLL the surface outflow consisted of well-mixed lagoon and ocean waters, however in the

larger ICOLL there appeared to be a dominant two layered flow. This implies that the

surface outflow consisted of predominantly fresher lake waters, which may have implications

of the ecology of the lake.

The daily exchange between each ICOLL and the ocean was dominated by the same

process, the mean flow (advective term), but at a longer timescale (weeks) the exchange

processes were different. On a daily basis, the ICOLLs are capable of transporting volumes

of water and water borne particles into and out of the system. A closer examination of the

actual daily exchange rates, illustrated that they were quite small (1-2 ppt cm s-1) when

compared to similar systems found elsewhere in the world, e.g. the Laguna de Terminos in

Mexico (David and Kjerfve 1998) and the San Juan Delta in Colombia (Restrepo and Kjerfve

2002) measured total net salt fluxes on the order of 101 and 102 ppt cm s-1, respectively. The

results from Wamberal Lagoon suggest that these daily exchange rates may change

throughout an opening period, thus it should be noted that the exchange rates may be

dependent on a range of environmental variables including, but not restricted, to the inlet

geometry, the wind climate, tidal forcing etc. The field data suggested that even though we

had a limited record, the lagoon could be flushed quite quickly (~4 days) during the two week

opening period.

At the longer timescale (weeks), the exchange process in the larger ICOLL (Smiths

Lake) became quite complex and different to the smaller ICOLL. In addition to tidal and

wind effects, Spring Tidal Pumping (STP) over the fortnightly tidal cycle also significantly

influenced the exchange in Smiths Lake. This finding suggested that there can be different

dominating processes driving the exchange in different ICOLL systems and that the length

of an opening event may be quite important for the overall exchange. In Smiths Lake, STP

was shown to promote fortnightly variations in the exchange, and the presence of mixed,

semi-diurnal tides promoted further variation in the exchange rates, from one spring - neap


cycle to the next. The resulting variation in flushing timescales ranged from 39 – 370 days,

which highlighted the importance of collecting a long data set when investigating the larger

ICOLL systems. By calculating a mean TER value for the entire spring neap cycle, the mean

flushing timescale was defined as approximately 113 days. Further field investigations into the

sub tidal processes in large ICOLLs are suggested to gain greater insight into the importance

of these processes.


CHAPTER 5

THE IMPORTANCE OF SUB TIDAL PROCESSES ON THE FLUSHING

AND EXCHANGE OF AN INTERMITTENTLY OPEN SHALLOW

COASTAL LAKE

5.1 Abstract

In shallow coastal lakes (and lagoons) the daily tides (high frequency motions) are often

ineffective in exchanging waters with the ocean; this is predominantly due to the presence of

a restricted or choked inlet. The low frequency or sub tidal processes thus become important

for the exchange between the lake and the ocean. In this paper the sub tidal transport

processes are examined in a small, shallow intermittently closing and opening coastal lake

(Smiths Lake, N.S.W.) using a three dimensional numerical model. Three different

combinations of sub tidal forcing (incorporating changes in mean sea level and variations in

local wind) are applied to the lake and compared with the sole effect of tidal forcing. The

results show that the exchange, regardless of the forcing, is dominated by a spring tidal setup

process, which promotes the net advection of waters into and out of the lake on a fortnightly

timescale. When sub tidal sea level forcing is also present, the peaks and troughs vary but

there is still a dominant sub tidal response, at the fortnightly scale. The flushing timescale of

the lake is similar under different natural forcing scenarios; however under more extreme

wind forcing (constant 6 m/s westerly wind) the flushing time is significantly longer

(approximately 60% more than with no wind). The release of a tracer, from a location on the

shoreline, illustrated that localised flushing is also largely controlled by the wind. In the

absence of wind, particulates in the surface waters are found in high concentrations, close to

the source and when wind is present, the transport of the tracer is greater and the


concentrations are lower due to dilution. Under more extreme wind conditions (constant

6ms-1 westerly wind), the tracer is constrained against the shoreline, at high concentrations.

5.2 Introduction

Coastal lakes and lagoons are often located in highly urbanised regions of the world and

can be subject to high loads of nutrients and pollution from the surrounding catchments.

The transport of waters between the lake / lagoon and the ocean is therefore important for

the health of the ecosystem, and residence time is a key variable determining if a particular

system will or will not suffer from eutrophication (Wolanksi et al. 2004). The tidal exchanges

are often predictable and continuous and constitute a reliable baseline for flushing (Smith

1993), but a restricted or choked inlet often hinders the exchange between many shallow

coastal lakes / lagoons and the ocean. In weakly forced tidal systems (micro tidal inlets), the

sub tidal forcing is often more effective in exchanging waters with the ocean than the tidal

currents (Holloway 1996, Janzen & Wong 1996, Hinwood et al. 2005), and therefore an

understanding of the sub tidal response of the lake / lagoon is important for understanding

the mean exchange rates and long term transport processes (Eguiluz and Wong 2005).

Sub tidal forcing is defined as those processes which have periods longer than the

dominant tidal periods (i.e. > 24hrs) may include: (1) remote forcing, which includes sea

level changes due to the passage of continental shelf waves (Griffin and Middleton 1991),

and (2) local forcing which includes local wind stress and freshwater inflows (Fernandes et

al. 2004). In the absence of freshwater inflows, as is the case in many coastal lakes and

lagoons in southern Australia, the wind may play a larger role in the exchange and flushing

(Valle-Levinson et al. 2001, Geyer 1997). These local and non-local forcing are less

predictable than the tides, as they are generated by meteorological forcing over the time


scale of days to weeks (Fernandes et al. 2004), leading to high variability over a short

timescale.

On a slightly longer timescale, the non-linear interaction between the first order tides (M2,

S2) can produce second order mean flows at the fortnightly timescale (Msf) (Ianniello 1977).

This is common in shallow waters and is often the explanation given to observed fortnightly

variations in currents and water levels. Another significant process operating at a fortnightly

timescale is the action of spring tidal pumping (Hinwood et al. 2005), which is the increase in

mean water level of a lake or lagoon due to spring tides. STP may occur in shallow lakes and

lagoons where the inlet cross sectional area varies significantly with depth. The difference in

channel depth, between the flood and the ebb tide, means that the ebb current flows through

a smaller cross section and encounters relatively higher resistance (Hinwood et al. 2005). This

process raisers the mean lake or lagoon water level. As the ratio of the ocean water level (tide)

to the channel depth increases so does the mean water level within the lake / lagoon and this

promotes a fortnightly tide. Characteristics of the fortnightly tide may also change due to

sedimentation of the inlet or changes to the tidal forcing (Hinwood et al. 2005). Hinwood et

al. (2005) defined this process as spring tidal pumping. However to delineate the process from

that of tidal pumping, here we will refer to the process as spring tidal setup. Earlier work by Hill

(1994) and Dias et al. (2000) has also identified a fortnightly variation in water levels in

lagoon systems.

To examine the effects of different sub tidal forcing on the flushing and exchanges

between shallow coastal lakes / lagoons and the ocean, an intermittently opening shallow

coastal lake, with a restricted inlet, was chosen as a field site. Along the southeast coastline of

Australia, many of the coastal lakes and lagoons experience intermittent openings to the

ocean, and one of the potential reasons for these openings can be to alleviate poor water

quality. Therefore the processes affecting flushing and exchange during this ‘opening period’

can often be critical in determining the resulting water quality of the water body. Smiths Lake


is located on the south east coast of Australia, has no significant river inflow and is relatively

shallow (< 5m) (Figure 5.1). The lake experiences limited exchange with the ocean, which can

vary from 1 to 4 months, at any one time.

This paper examines the exchange and flushing characteristics under different sub

tidal forcing (tidal only, local wind variations and mean sea level changes) at Smiths Lake

through the application of a three dimensional Estuary and Lake Computer Model

(ELCOM).

5.3 Methods

5.3.1 Study site

Smiths Lake (Figure 5.1) is located approximately 280 km north of Sydney, Australia

and has a waterway surface area of 11 km 2, a catchment area of 32 km 2 and a maximum

depth of ~ - 4 m, when open (Webb et al. 1998). The duration of the opening to the ocean

varies from 1 - 4 months, and for the remainder of the year, the lake is isolated from the

ocean. The average interval between openings is approximately 18 months. The majority of

the opening events are artificial, to mitigate flooding of nearby properties, and are induced

when internal water levels reach 1.7 - 2.1 m AHD (Webb et al. 1998). The inlet connecting

the lake to the ocean is approximately 60 m wide (at its maximum), -1.0 m deep (Webb et al.

1998), and experiences high tidal choking (tidal range is reduced by 90% (section 4.4.3).


Figure 5.1 Smiths Lake, bathymetry, and model transect outputs (transects 1 and 2) and

profile output locations (P1, P2 and P3).

5.3.2 The numerical model

The Estuary, Lake and Coastal Ocean Model (ELCOM) is a three-dimensional

hydrodynamic model used for predicting velocity, temperature and salinity distribution in

water bodies. The transport equations are the unsteady Reynolds averaged Navier-Stokes

(RANS) and scalar transport equations using the Boussinesq approximation and neglecting

the non-hydrostatic pressure terms (Hodges 2000). The surface thermodynamics are

governed by bulk transfer models (Hodges 2000) and a Euler – Lagrange scheme is used to

solve momentum advection, while advection of scalars uses the conservative flux limiting,

explicit differentiation scheme, Ultimate – Quickest (Laval and Imberger 2003). The model

uses a finite-difference grid and the vertical mixing is governed by a 3D mixed layer approach

(Imberger and Patterson 1990). The model applies a separate mixed layer model to each

water column, specified by the 3D grid, to provide vertical turbulent transport, and the 3D


transport moves the total kinetic energy (TKE) around making it available for vertical mixing

(Hodges 2000). The model has been successfully applied to estuarine environments (Robson

and Hamilton 2004, Chan et al. 2003), and lake environments (Romero et al. 2004; Appt et al.

2004; Hodges et al. 2000) as well as exchange flows through straits (Laval and Imberger

2003) subjected to external environmental forcing such as wind stress, surface heating or

cooling.

5.3.3 Model set-up

The bathymetry for Smiths Lake consisted of a grid containing 134 x 225 cells with

uniform spacing of 25 m. The vertical resolution consisted of 20 layers with a vertical spacing

of 0.5 m. The time step was 10 seconds to allow for baroclinic stability. The inlet was defined

as the only open boundary and was forced by observed ocean water levels (barotropic

forcing) with a set salinity (35 ppt) and temperature (20oC) (baroclinic forcing). The inlet

channel was 2 grid cells wide (total of 50 m) and had a mean depth of 0.75 m. The edges of

the lake were classified as slip boundaries and the bottom friction, over the entire lake, was

defined by a constant drag coefficient of 0.005. The bottom drag coefficient agrees well with

the value of 0.0041 +/- 0.002 obtained from field data in a choked lagoon in Sri Lanka

(Rydberg and Wickbom 1996). Coriolis effects were included and the model results were

output every hour.

5.3.4 Model Validation

The model was validated against a period of field data for the first two weeks of an

opening event in May 2003. During the simulation the system was forced with the observed

meteorological forcing for the specified time period (wind, solar insolation, air temperature,

rainfall, humidity, atmospheric pressure). The model predictions of hourly water levels, from


locations P1, P2 and P3 (Figure 5.1) compared well to those of field data (Figure 5.2 (a)), (r2

= 0.84). The over prediction of the higher water levels, in the model (Figure 2b) occurred at

the onset of the opening event and suggests the model is not capturing the outflow correctly.

This may be due to the inlet geometry, which was set to constant throughout the model runs,

when in reality the inlet would be changing quite dynamically during the first 24 hours. The

remaining small variations were most likely due to natural localised variations in the wind,

experienced in the lake, but not experienced in the model (due to a lack of spatial variation in

the applied wind field). A similar r2 (0.89) value was observed when field data from two

different locations within the lake were compared. A harmonic analysis on both data sets (not

shown here) revealed that the tidal amplitudes and phases matched well, even though the

amplitudes were small (~ 0.1 – 0.2m).

Figure 5.2 Model validations (a) water levels from the model output and the field data,

(b) water level comparison, and (c) mean hourly velocities from the field and the model


output, where positive is flowing into the lake and negative is flowing out of the lake. The

model output data and field data are from location P1 (Figure 5.1).

A comparison of the mean hourly velocities showed some variation between the field

data and the model (Figure 5.3 (c)). This, again, may be due to variations between the natural

wind field and the applied wind field in the model. Both the field and the model data show

the initial outflow, after opening (16th May), and then the presence of the twice daily flood

tide peaks (semi diurnal system) on the 17th and 18th May, 2003.

5.3.5 Model scenarios

Four predictive model simulations were undertaken to examine the sub tidal

processes acting on the lake. The initial conditions for all simulations were the same and

consisted of a well-mixed lake with a mean salinity of 15 ppt (observed in the field). For the

first simulation, the tidal (< 24 hrs) forcing was isolated from an observed ocean water level

data set (through high pass filtering of the observed data set) and was applied as an open

boundary forcing to the lake (Figure 5.3). The length of the record was 16 days allowing both

spring and neap tides to occur, and should allow a spring tidal setup to be observed, due to

the process being a function of the tidal forcing (< 24 hrs) and the bathymetry of the lake.

For the second simulation, the sub tidal component (> 24 hrs) was retained in the observed

ocean tidal water levels data set. For the third simulation, a natural variable wind record was

obtained from local meteorological data and was applied as a forcing condition. For the

fourth simulation a constant westerly wind of 6 m s-1 was applied to the lake. This wind

direction was chosen as a representative wind as westerly winds are common during the

winter months, along the south east coast of Australia (Gentilli 1972), which also coincides

with the timing of the last two openings of Smiths Lake. A westerly wind is also orientated in

the direction of outflow from the inlet, and therefore may restrict the inflow of oceanic


waters and resulting exchange or flushing. The forcing conditions associated with the various

simulations are summarized in table 5.1.

Tidal Sea Level changes

Variable Wind

Constant Wind

Tidal only (Simulation 1) X

Tidal and Sea Level (Simulation 2) X X

Variable wind (Simulation 3) X X X

Constant 6 ms-1 westerly wind (Simulation 4) X X X

Table 5.1 Different forcing combinations for the modelling simulations


Figure 5.3 Boundary forcing for the scenario modelling: (a) Tidal forcing only, (b) Sea

level changes, and (c) observed variable wind climate.

5.3.6 Quantifying the exchange

To quantify the exchange, the water volume and salt flux through a model cross

section can be extracted; where the water volume flux (QV) and the salt flux (QS) are defined

as:

∫=A

V dAUQ . (5.1)

and

∫=A

S dASUQ . (5.2)

where A is the cross sectional area in the direction of flow, U is the mean velocity of the

cross section, and S is the mean salinity of the cross section. These fluxes were calculated for

every cell face in the cross section and then summed together to provide a net flux. The

location of transect 1 was selected to account for fluxes into and out of the main body of the

lake. The region between transect 1 and the inlet was quite shallow, resulting in numerical

problems with calculation of fluxes, and the deeper region in the north eastern corner often

becomes quite isolated, at low water levels and therefore has not been included in the flux

calculations. The tidal and sub tidal water levels (low pass filtered at 26hrs) and the fluxes

were calculated across transect 1 (Figure 5.1), for each of the model simulations.



5.4.1 Salt wedge intrusion

The intrusion of the salt wedge showed a variation in timing and extent for the four

different simulations (Figure 5.4). The slight variations on a short timescale (hours) as seen in

the results may be due to numerical noise due to the short time step (seconds) and output of

the data (hourly), however there are general trends that may be described as follows. The

profile of salinities was recorded at P3 (Figure 5.1) over the 16 days, and the results showed

the salt wedge intruded the furthest under the tidal forcing only simulation (simulation 1,

Figure 5.4a). In comparison, when mean sea level changes were incorporated into the

boundary forcing (simulation 2, Figure 5.4b), the salt wedge intrusion was hindered, with the

24 ppt contour line lagging by 1 day and the 28ppt contour line lagging by approximately 4

days.


Figure 5.4 Salt wedge intrusion rates for all four simulations. Salinity profiles were

recorded at location P3 continuously over the 16 day period. The simulations are as follows

(a) Tidal forcing only, (b) Tidal and sea level changes, (c) variable wind, and (d) constant

wind. The line [A] and the line [B] show corresponding contours within the first three

scenarios, and highlight the greater variation in timing towards the end of the model runs.

Under the variable wind scenario (simulation 3, Figure 5.4c), the salt wedge intrusion

was further restricted, and the 24ppt contour line exhibited a lag of 2 days behind simulation

1. However for the 28 ppt contour line there was a lag of approximately 7-8 days, when

compared to simulation 1. The variation in timing of the contour lines, between the first

three simulations, was only 2-3 days in the first week however by the second week the

variation in timing was approximately 7 days. This suggested that the variations in forcing

between the different simulations had a greater effect on the intrusion and exchange during

the second week of the simulation. Under the more extreme forcing (a constant westerly

wind, simulation 4) the salt wedge was arrested completely, in the inlet channel (not shown),

with the western basin appearing vertically well mixed by day 16 (Figure 5.4d).

5.4.2 Exchange characteristics

The sub tidal volume and salt fluxes (Figure 5.5), showed a distinct split in the

groupings of the scenarios. The water levels, sub tidal water volumes and salt fluxes in the

tidal forcing only simulation (simulation 1) and the constant wind simulation (simulation 4)

showed a good correlation with the spring neap tidal cycle (Figure 5.2 (a)), with the peak

(trough) in the water levels corresponding with the spring (neap) tides. In the tidal forcing

only simulation, there was no external sub tidal forcing; this suggests the sub tidal water levels

and fluxes may have been driven by friction or bathymetric effects within the lake and the

response is most likely due to the process of spring tidal set-up, dominating the exchange.


The sea level changes simulation (simulation 2) and the variable wind simulation

(simulation 3) showed greater variability throughout the 16 day period, with a lesser peak in

both water volume and salt fluxes, around the time of spring tides (days 2 - 4) and a second

peak around day 10 (Figure 5.5), coinciding with the peak in mean sea level (Figure 5.2). This

suggested that whilst the tidal forcing produced the spring tidal set-up within the lake, the

variations in mean sea level also affected the exchange of waters between the lake and the

ocean. In the constant wind model simulation, the second peak, due to the mean sea level

set-up, was not observed; even though mean sea level changes were incorporated into the

boundary forcing. This suggested that under constant wind the effects of mean sea level

changes might be negated.


Figure 5.5 Exchange fluxes for Smiths Lake, where positive is into the lake and negative

is out of the lake (a) the spring neap tidal forcing, (b) sub tidal water levels, (c) sub tidal water

volume fluxes, and (d) sub tidal salt fluxes, for all four simulations

5.4.3 Flushing timescales

There are two types of flushing timescales that allow a comprehensive investigation

of the lake and will encompass the effects of any stratification (Monsen et al. 2002). These

include (i) a system wide flushing timescale, which produces a value for the entire lake; and

(ii) a local flushing timescale, which will highlight regions of low flushing (high residence

time).

5.4.3.1 System wide flushing

To examine the system wide flushing of the lake, the flushing time can be estimated

as the time for a tracer mass to reduce to a certain level of the initial mass (e.g. 1/e), this is

often termed as the e-folding time (Choi and Lee 2004). As the tracer mass decreases with

time, it is assumed to follow an exponential decay and thus an exponential curve can be fitted

to the data:

teY βα= (5.3)

where Y is the percentage of original lake water (tracer mass), α and β are constants and t is

time in days.

For the first 4 days, all 4 simulations were similar in flushing (Figure 5.6). From day 5

onwards, the constant wind simulation experienced a longer flushing time, whilst there were

only small variations between the other 3 simulations. The flushing timescale (e-folding time,

Figure 5.6) for the first two simulations was approximately 14 days, the variable wind

simulation was slightly longer at 16 days and the constant wind simulation had not reached


the e-folding time by the end of the simulation (calculated to be 26 days, equation 5.6). These

results assumed all water entering on the flood is new seawater, and no returning lake water,

therefore must be taken as the shortest possible time required for flushing. For example,

previous research (Chapter 4) have shown that calculations taken during one week of neap

tides (2 months after the opening), showed approximately 18% of the water returning on the

flood tide may be old lake water, suggesting that under natural conditions the flushing

timescale would become slightly longer.

Figure 5.6 System wide flushing times for Smiths Lake, under the four different

scenarios.

During all four simulations, the fraction of exchange was greater during the first eight

days (spring tides), than the last eight days (neap tides). By calculating the ratio of the neap

against the spring flushing concentrations, it was found that all four simulations showed a


stronger flushing potential during the spring tides, which accounted for ~ 70% of the total

flushing over the 16 days with the neap tides only accounting for ~ 30% of the total flushing

potential. The longest flushing timescale was found with the constant westerly wind, which

reduced the flushing potential by ~ 35%. This may be due to the direction of the wind

restricting inflow of oceanic waters, and therefore not allowing flushing of the main body of

the lake. It should be remembered that the flushing timescale is dependent on the percentage

of old lake water still remaining, therefore with no new ocean water entering, the old lake

water would remain at a high percentage and produce a high flushing timescale.

5.4.3.2 Local Flushing

To examine the local flushing characteristics, the retention times (RT) of water

parcels within the lake were examined. This method can highlight regions of the lake that

may experience low flushing (high RT). In the model, at the beginning of the simulation each

cell is given a water age of zero, each cell is then incremented by the actual time during each

time step. Any water entering the domain is given an age of zero. The water is then

transported as a valid transportable scalar.

The results from the first three simulations showed that the surface layer had a longer

retention time than the bottom waters within the lake (Figure 5.7, (a)). This may have been

due to the inflowing sea water accumulating at the bottom of the lake near the inlet channel,

resulting in smaller retention times. The bottom waters had a retention time (~ 7 days) half

that of the surface waters (~ 14 days), and during the constant wind simulation (Figure 5.7

(b))) the waters in the middle and western basin experienced a retention time between 12 –

14 days, exhibiting the poorest localised flushing of all the simulations.

To investigate the local flushing response, a tracer was released continually

throughout each model run, from a site located on the northern edge of the lake (Figure 5.8).

The conservative tracer was contained within a freshwater inflow, which entered the lake via


a surface edge grid cell, and may be representative of particles entering the lake via a storm

water drain. The flow rate was 0.5 m3 s-1 and the initial tracer value was set to 100. The

resulting concentrations within the lake could then be examined as a direct percentage of the

original inflow value.

Figure 5.7 Two west – east transects (transect 2, Figure 5.1) through Smiths Lake

showing retention times (in days) after 16 days in (a) the tidal only model simulation, and (b)

the constant westerly wind model simulation

Under tidal forcing only (simulation 1) the tracer was located predominantly in the

surface waters, with negligible values (< 1%) found in the bottom waters (Figure 5.8). After

16 days, there were values up to 20% in the immediate vicinity of the outflow (< 50 m) whilst

concentration values in the rest of the lake were no greater than 10% (Figure 5.8). Spatial

variations in the flow of the tracer illustrated that tracer 1 was focused in the northern half of

the lake for all four of the model simulations.


Figure 5.8 Tracer 1 concentrations in the surface waters after 16 days, in the following

model simulations: (a) tidal only, (b) tidal and sea level changes, (c) variable wind, and (d)

constant westerly wind. North is aligned with the y-axis. An arrow on the northern edge of

the lake indicates the location of the tracer release.

Under tidal forcing only (Figure 5.8 (a)), the tracer was predominantly transported

south of the dispersal site and into the western basin of the lake. With the addition of sea

level changes (Figure 5.8 (b)) the tracer followed a similar transport pattern, however greater

concentrations were found further from the dispersal site than in the tidal forcing only model

run, with concentrations of 8 % found approximately 1 km from the dispersal site. The

greatest transport of the tracer was found when variable wind forcing was added to the

model run (Figure 5.8 (c)), which allowed the tracer to reach the inlet mouth by the 16th day,

however the values were still at 10 % or less in the majority of the lake. Under constant

westerly wind (Figure 5.8 (d)); the tracer release was constrained by the wind to the northern

and eastern edges of the lake. This allowed higher concentrations to develop (approximately

14 %) in the near shore region (up to 250 m) of the tracer dispersal site, with negligible values


in the rest of the lake. It was however, the only scenario model run to show up similar tracer

levels in the bottom and surface waters, most likely due to the lack of vertical stratification

(section 3.2).

5.4.4 Variations in exchange and flushing

The mixing of waters, salinity structure, sediment transport and flushing of chemical

constituents all vary with the volume of seawater entering the lake. Due to the

unpredictable nature of the sub tidal forcing (wind, mean sea level changes, fortnightly

variations in the spring neap cycle), variations in the exchange characteristics will not be

uniform at the sub tidal timescale. It must also be noted that rainfall has not been included

in these scenarios, and this would also affect the exchange and flushing. Even though wind

induced currents are widely acknowledged in playing a key role in removing contaminants

from semi enclosed lagoons (Mathieu et al. 2003), in this case the extreme wind condition

(constant wind model run) greatly hindered the exchange, but the natural wind (variable

wind run) had little influence on the flushing. This variation in forcing may lead to a highly

dynamic ecosystem, where the timing and variation in water levels and exchange can have

considerable effect on the ecology. For example, the spawning of many marine organisms

are known to be influenced by the timing of high water levels in their habitat (Hill 1994).

The variations in the exchange also play a key role in defining the flushing timescale

of the lake. This was observed in the constant wind simulation, where after 16 days, there

was a 20% decrease in flushing, when compared to the other simulations. This most likely

occurred because the direction of wind that was chosen was orientated in the direction of

outflow, which therefore restricted inflow of ocean waters and subsequent flushing.

Previous research by Webster and Harris (2004) identified the high sensitivity of

intermittently opening lake and lagoon systems to changes in the flushing, on a short


timescale, which can lead to increasing and decreasing nutrient loads. Scanes (2002) has

noted that if high nutrient concentrations are not dispersed within tens of hours then

nuisance levels of algae can be established, suggesting that the localised flushing may be

extremely important for the health of the lake. Also because the flushing process (Figure

5.6) is not linear, and an opening event can vary in duration, there may be considerable

variability in the flushing process from one opening event to the next. The longer retention

times of the surface waters and the ability of the lake to retain higher concentrations of a

released tracer during low wind conditions will also play a key role in defining the ecology

of the lake, as in stratified systems; the surface layer is where most primary production

takes place (Stocker and Imberger 2003).


The four simulations, of Smiths Lake, provided insight into the flushing and exchange

characteristics of this shallow coastal lake and suggest that there may be large temporal and

spatial variability in these characteristics during an opening event. Based on these results we

conclude that:

1) Sub tidal forcing (sub tidal sea level forcing, variable wind) hinders the intrusion of

the salt wedge (initial exchange) into the main body of the lake, whilst under more

extreme conditions (constant westerly wind) the exchange is restricted to the inlet

channel.

2) The sub tidal exchanges between the lake and the ocean are driven predominantly by

a spring tidal set-up that promotes the pumping of waters into (out of) the lake

during spring (neap) tides. This produces a fortnightly variation in water level and

exchange, and when sub tidal sea level forcing was also present, the peaks and

troughs varied, but there is still a sub tidal response. The presence of natural wind

conditions (variable wind) appears to have no influence on this process, however


under more extreme conditions (constant westerly wind), the timing of the peaks may

vary.

3) Greater flushing of the lake occurred during spring tides, as opposed to neap tides,

with little variation in the overall flushing time (14-16 days) under natural conditions

(variable wind, tidal and sub tidal sea level forcing). Under more extreme conditions

(constant westerly wind) the flushing time is greatly reduced (26 days).

4) The localised flushing is largely controlled by the wind. In the absence of wind,

particulates in the surface waters are found in high concentrations, with no preferred

direction of net transport, however when wind is present, the net transport is greater,

but the concentrations, at any one location, within the lake, are lower. However,

under extreme wind conditions (constant 6ms-1 westerly wind), the localised flushing

decreases significantly and is constrained, against the edges of the lake, by the

orientation of the wind.


CHAPTER 6

CONCLUSIONS

6.1 Summary

The mixing and circulation of waters within and between coastal lagoons and the ocean

are extremely important for the health of the ecosystem. Therefore the objectives of this

study were to gain a detailed understanding of the hydrodynamics of intermittently closing

and opening lakes and lagoons. This was achieved through the use of field data and

numerical modelling, where a detailed investigation was completed examining the

hydrodynamics, of two contrasting ICOLL systems, in both the open and closed state.

The examination of the vertical mixing processes, using field data analysis (chapter 3),

demonstrated that there was large temporal variability in the timing and magnitude of the

processes driving stratification / de-stratification events, within the two ICOLL systems

(figure 6.1). The results showed that the smaller ICOLL, Wamberal Lagoon, was susceptible

to periods of stratification during both the closed and the open states. During the closed

state, periods of rainfall, low wind and/or high solar insolation led to short (< 3 days) and

irregular stratification events (section 3.3.1), whilst during the open state, stratification events

occurred through a combination of rainfall, low winds and variations in tidal mixing (section

3.3.3). There was a tendency for dissolved oxygen to decrease, in the bottom waters, when

the Buoyancy frequency was > 0.1 s-1 (section 3.3.4).


Figure 6.1 Conceptual models of the physical forcing present within a) closed and b)

open ICOLL systems.


The larger ICOLL, Smiths Lake, demonstrated higher vertical stability and exhibited a

tendency for persistent stratification, during both the closed and open states, primarily due

to solar insolation (closed state) and gravitational circulation (open state), respectively

(section 3.3.1). The persistent stratification maintained a vertical gradient in dissolved oxygen

between the surface and bottom layers. However, spring tidal pumping associated with

fortnightly tides appeared to promote isolation of the bottom waters, causing the dissolved

oxygen rates to temporarily decrease (for approximately 5 days) during the neap cycle

(section 3.3.4). This research established that both small and large ICOLLs can exhibit

temporal variability in vertical mixing processes, which also has an immediate response in

the dissolved oxygen concentrations; especially within the smaller ICOLL (section 3.3.4),

and under the right environmental conditions anoxia may develop.

An examination of the horizontal processes (chapter 4) demonstrated that tidal and

wind effects controlled the circulation in both of the ICOLLs, even though one was

predominantly well mixed and the other was predominantly stratified (section 3.3.3.3). The

mean circulation set-up exhibited a residual flow exiting the ICOLL at the surface, with

minimal inflow at depth (figure 4.2, figure 4.5), unlike the typical gravitational circulation set-

up (figure 2.4) observed in most estuaries. Whilst the surface waters exhibited greater mean

currents, the modelling work (chapter 5) showed that in the larger ICOLL, the surface waters

had a longer retention time than the bottom waters (section 5.4.3.2). An examination of the

localised flushing of the surface waters (indicated by the release of a tracer) showed that the

transport was restricted to the surface waters (section 5.3.4.2), and in the absence of any local

winds there were higher concentrations (of the tracer) closer to the source, with no preferred

direction of net transport. When local winds were introduced, the transport of the tracer

away from the point source was greater leading to lower concentrations within the lake. This

research showed that the localised flushing within an ICOLL varied spatially, dependent on

climatic conditions.


Barotropic motions drove the movement of water between the ICOLL and the

ocean, otherwise known as the exchange, in both systems. The smaller ICOLL was

dominated by tidal and wind effects, whilst the larger ICOLL, in addition to tidal and wind

effects, exhibited a spring tidal set-up process over the fortnightly tidal cycle which also

influenced the exchange (chapter 4). This was confirmed by the spectral density plot (figure

4.7) and the observed variations in water masses occurring at the sub tidal timescale (figure

4.10). This was the first research to differentiate that different processes can dominate the

exchange of waters, between an ICOLL and the ocean.

The dominance of the low frequency or sub tidal transport within Smiths Lake, led to

a closer examination of the sub tidal transport (circulation, exchange and flushing) processes,

using three-dimensional numerical modelling (Chapter 5). The modelling work was the first

to successfully reproduce the fortnightly variation in water level and exchange, associated

with the spring tidal set-up, using actual bathymetry and observed meteorological forcing.

The results demonstrated that the exchange, in the presence and absence of external sub tidal

forcing (wind variations and changes in mean sea level), was always dominated by the action

of the spring tidal set-up (section 5.3.3). This promoted the net advection of waters into and

out of the ICOLL on a fortnightly timescale (figure 5.5). This finding suggested that simple

tidal prism models could not be used to quantify the flushing of larger ICOLLs, and that a

different data analysis technique would be needed to encompass the spring neap fortnightly

variations in exchange.

To examine the flushing timescales of the two ICOLLs, two methods were

compared. The first method used a modified flushing timescale and was calculated using field

data (section 4.3.6); the second method used a tracer release in the numerical model and

values were obtained under a range of different external forcing scenarios (section 5.3.4). The

field data suggested that even though the two ICOLLs experienced different exchange

characteristics, the timescale of flushing was comparable to the duration of opening, ranging


from days in the smaller ICOLL to months in the larger ICOLL (section 4.3.6). The

modelling data (only calculated for the larger ICOLL) demonstrated slightly smaller flushing

timescales (section 5.3.4.1), and the variations between the two timescales may be attributed

to a number of factors including, a) the absence of rainfall / runoff in the modelling

scenarios, and b) the lack of spatial and temporal variation within the field data analysis (data

was collected from one location, over a week). The combination of these two factors suggest

that the actual timescale may lie somewhere between the two values, still resulting in a

timescale of months for the larger ICOLL. The modelling work also demonstrated that the

flushing timescale varied little under different natural variations such as wind variations and

changes in mean sea level (section 5.3.4.1). Further, it was noted that greater flushing of the

ICOLL occurred during spring tides, as opposed to neap tides (section 5.3.4.1) and that

under a more extreme scenario, such as constant wind forcing, the flushing time did change,

increasing by approximately 60%.

The research has shown that when ICOLLs are open to the ocean they do not

conform to typically estuarine characteristics (mean circulation, exchange characteristics,

vertical mixing regimes), and during both the open and closed state, the hydrodynamics can

be highly variable due to shallow depths and variations in external forcing.

6.2 Recommendations for future work

6.2.1 Transition between open and closed state

The transition phase between the open and the closed state illustrated complex

dynamics in Wamberal Lagoon (section 3.3.3). The inlet closed on the 28th May, and the field

data captured the entire closing event. During the days previous to the 28th, the tidal

velocities decreased, a rainfall event occurred and there was an increase in water level. The

combination of these three events, we believe, led to the instant vertical stratification that was


observed. However it would be interesting to undertake a field based study on the processes

occurring when the inlet closes, especially focusing on how the decrease in tidal velocities

may affect the vertical mixing. The presence of vertical mixing was very important for the

maintenance of healthy dissolved oxygen concentrations within the smaller ICOLL and slight

decreases in the magnitude and variations in the timing of the mixing appears critical to the

dissolved oxygen levels.

6.2.2 Rainfall Events

The presence of rainfall provides a freshwater input to the surface waters that

introduces a vertical density gradient. The ability of the ICOLL to mix the fresher surface

waters with the underlying saltier waters then depends on the mixing processes present. It

became obvious, from the field data from the smaller ICOLL, that under certain sized rainfall

events, an open lagoon showed the ability to produce quite strong vertical stratification on a

short timescale. No large rainfall events were observed at the larger ICOLL, Smiths Lake,

however if equations 3.3 and 3.4 hold true then a rainfall event of a certain magnitude could

produce strong stratification within the larger ICOLL as well. If strong stratification was

produced, the exchange dynamics may change. This may also have important implications for

the dissolved oxygen response. It should also be noted that freshwater runoff was not

investigated in this research, however whilst undertaking field work it became obvious that

freshwater fronts were entering the lake during one of the rainfall events, and these may play

an important role in the horizontal and vertical transport of waters within the lake. An

intensive field based study during a large rainfall event would clarify these interactions.


6.2.3 Spring tidal pumping

The larger ICOLL, Smiths Lake, exhibited spring tidal pumping which dominated the

exchange between the lake and the ocean (section 5.3.3). This was not observed in the

smaller ICOLL, Wamberal Lagoon, and the reason for this may be twofold, firstly the smaller

ICOLL was not open long enough for any adequate data analysis to define spring tidal

pumping (14 days), and secondly the flushing and exchange occurred quite quickly (days),

therefore any fortnightly variations in salinity would have been negligible. If we assume that

these two ICOLLs are examples of the two different types of exchange, then there must be a

transition zone between these two systems, where the exchange characteristics may be

entirely different again. It is also not known if the spring tidal pumping would have the same

exchange characteristics whether the lake was vertically well mixed or stratified. These are

important questions when it comes to trying to understand the flushing and exchange

characteristics of ICOLLs and a longer field based study would help to clarify these issues.

6.3 Final note

Together with the field data analysis and the numerical modelling, the results shown here

are the first to document the hydrodynamics of two contrasting ICOLL systems during the

open and closed states. The results highlight some of the key differences between large and

small ICOLLs as well as identifying the large spatial and temporal variability that may be

present. Overall this thesis provides a greater understanding of the hydrodynamics of ICOLL

systems; and is a relevant baseline study for future detailed work on the physical processes or

the ecology of these systems.


BIBLIOGRAPHY

ANZECC (2000). Australian and New Zealand Guidelines for Fresh and Marine Water

Quality, Volume 1, The Guidelines (Chapters 1-7) Australian and New Zealand

Environment and Conservation Council (ANZECC) and Agriculture and Resource

Management Council of Australia and New Zealand (ARMCANZ), Paper No. 4 -

Volume 1 (Chapters 1-7)

Appt, J., Imberger, J. and Kobus, H. (2004). Basin-scale motion in stratified Upper Lake Constance. Limnol. Oceanogr., 49: 919-933

Banas, N.S., Hickey, B.M., MacCready, P. and Newton, J.A. (2004). Dynamics of Willapa

Bay, Washington, a highly unsteady, partially mixed estuary. J. Phys. Oceanogr., 34: 2413

– 2426

Bonilla, S., Conde, D., Aubriot, L. and Del Carmen Perez, M. (2005) Influence of hydrology

on phytoplankton species composition and life strategies in a subtropical coastal lagoon

periodically connected with the Atlantic Ocean. Estuaries. 28: 884-895

Borsuk, M.E., Stow, C.A., Luettich, Jr. R.A., Paerl, H.W. and Pinckney, J.L., (2001) Modelling

oxygen dynamics in an intermittently stratified estuary: estimation of process rates using

field data. Estuar. Coast. Shelf Sci., 52: 33 - 49.

Bruun, P. (1986). Morphological and Navigational Aspects of Tidal Inlets on Littoral Drift

Shores. Journal of Coastal Research., 2 : 123-145.

Chan, T.U., Hamilton, D.P., Robson, B.J., Hodges, B.R. and Dallimore, C.J. (2002). Impacts

of hydrological changes on phytoplankton succession in the Swan River, Western

Australia. Estuaries, 25: 1406 - 1415

Choi, K.W. and Lee, J.H.W. (2004). Numerical determination of flushing time for stratified

water bodies. J. Mar. Systems., 50: 263 - 281


Collett, L.C., Collins, A.J., Gibbs, P.J. and West, R.J. (1981). Shallow dredging as a strategy

for the control of Sub littoral Macrophytes: a case study in Tuggerah Lakes, New South

Wales. Aust. J. Mar. Fresh. Res., 32 : 563-571

David, L.T. and Kjerfve, B. (1998). Tides and currents in a two-inlet coastal lagoon: Laguna

de Terminos, Mexico. Cont. Shelf. Res., 18: 1057 – 1079

Dias, J.M., Lopes, J.F., Dekeyser, I. (2000). Tidal propagation in Ria de Aveiro Lagoon,

Portugal. Phys. Chem. Earth (B), 25: 369-374

DNR, (2006). Department of Natural Resources, N.S.W. website

http://www.dlwc.nsw.gov.au/care/water/estuaries/estuaries.html

DNR, (2004). Discussion Paper: ICOLL Management Guidelines. Department of Natural

Resources, N.S.W. Australia

Dye, A. and Barros, F. (2005). Spatial patterns of macrofaunal assemblages in intermittently

closed / open coastal lakes in New South Wales, Australia. Estuar. Coast. Shelf Sci., 64:

357-371

Dyer, K. (1997). Estuaries: A Physical Introduction. 2nd Edition. John Wiley & Sons. Ltd.

Eguiluz, A. and Wong, K-C. (2005). Second order tidally induced flow in the inlet of a coastal

lagoon. Estuar. Coast. Shelf Sci., 64: 509-518

Farrow, D.E. and Patterson, J.C. (1993). On the response of a reservoir sidearm to diurnal

heating and cooling. J. Fluid Mech., 246: 143-161

Fernandes, E., Tapia, I., Dyer, K., Moller, O. (2004). The attenuation of tidal and sub tidal

oscillations in the Patos Lagoon estuary. Ocean Dyn., 54 : 348-359

Fischer, H.B., List, E.J., Koh, R.C.Y., Imberger, J. and Brooks, N.H. (1979). Mixing in Inland

and Coastal Waters. 483 pp, Academic Press, San Diego, California.


Friehe, C.A. and Schmitt, K.F., (1976). Parameterization of air-sea heat fluxes of sensible heat

and moisture by bulk aerodynamical formulas. J. Phys. Oceanogr., 6: 801-9

Gentilli, J. (1972). Australian Climate Patterns. Thomas Nelson (Australia) Limited.

Geyer, W.R., (1997). Influence of wind on dynamics and flushing of shallow estuaries.

Estuar. Coast. Shelf Sci., 44: 713-722

Geyer, W.R., Morris, J.T., Prahl, F.G. and Jay, D.J. (2000). Interaction between physical

processes and ecosystem structure: A comparative approach. In ‘Estuarine Science, a

synthetic approach to research and practice’. (Hobbie, J.E. Ed), 177-206 pp

Gonenc, E., Wolflin, J.P. (2005). Coastal Lagoons: ecosystem processes and modeling for

sustainable use and development. Boca Raton, CRC Press.

Gordon, A. D. (1990). Coastal Lagoon Entrance Dynamics. Proceedings of the

International Conference on Coastal Engineering 3, 2880-2893.

Griffin, D.A., Middleton, J.H. (1991). Local and remote wind forcing of New South Wales

Inner Shelf Currents and Sea Level. J. Phys. Oceanogr., 21: 304-322

Griffiths, S.P. (2001). Factors influencing fish composition in an Australian intermittently

open estuary. Is stability salinity-dependent?. Estuar. Coast. Shelf Sci., 52 : 739-751

Groen, P. (1969). Physical Hydrology of Coastal Lagoons. In Coastal Lagoons: A

Symposium. Memoir of the International Symposium on coastal lagoons. UNAM –

UNESCO, Mexico, D.F. November 28-30th, 1967

Gonenc, E. and Wolflin, J.P. (2005). Introduction, In ‘Coastal Lagoons: ecosystem processes

and modeling for sustainable use and development’. (Gonenc, I.E. and Wolflin, J.P. Eds)

Chapter 1, Boca Raton, CRC Press.


Gurel, M., Tanik, A., Russo, R.C. and Gonenc, I.E. (2005) Biogeochemcial cycles. In ‘Coastal

Lagoons: ecosystem processes and modeling for sustainable use and development’.

(Gonenc, I.E. and Wolflin, J.P. Eds) Chapter 4, Boca Raton, CRC Press.

Haines, P.E., Tomlinson, R.B. and Thom, B.G. (2006) Morphometric assessment of

intermittently open/closed coastal lagoons in New South Wales, Australia. Estuar. Coast.

Shelf. Sci., 67: 321- 332

Hearn, C.J. and Robson, B.J. (2001). Inter-annual Variability of Bottom Hypoxia in Shallow

Mediterranean Estuaries. Estuar. Coast. Shelf Sci., 52: 643-657

Hearn, C.J. (1995). Water exchange between shallow estuaries and the ocean. In ‘Eutrophic

shallow estuaries and lagoons’, CRC Press, (McComb, A. Ed), 151-172 pp

Herzfeld, M., Hamilton, D.P. and Douglas, G.B., (2001). Comparison of a mechanistic

sediment model and a water column for hind casting oxygen decay in benthic chambers.

Ecological Modelling., 136:255-267

Hill, A.E. (1994). Fortnightly Tides in a Lagoon with Variable Choking. Estuar. Coast. Shelf

Sci., 38: 423 – 434.

Hinwood, J., McLean, E. and Trevethan, M. (2005). Spring Tidal Pumping. In the Proc.

Coasts and Ports Conference: Coastal Living – Living Coast, Adelaide, South Australia,

Australia, 601-606.

Hodges, B.R. (2000). Estuary, lake and coastal ocean model (ELCOM): user manual,

University of Western Australia, Centre for Water Research, University of Western

Australia.

Hogg, A.M., Ivey, G.I. and Winters, K.B. (2001). Hydraulics and mixing in controlled

exchange flows. J. Geophys. Res. 106 (C1): 30,695-30,711


Holloway, P. (1996). A field investigation of water exchange between a small coastal

embayment and an adjacent shelf. In: Pattiaratchi, C.B. (ed) Mixing in Estuaries and

Coastal Seas, Coastal and Estuarine Studies 50, pp 145-158

HR Wallingford, (1994). Wamberal Lagoon Breakout Investigation: Telemac Application.

Report EX 3088. HR Wallingford Ltd. Howbery Park, Wallingford, Oxfordshire, United

Kingdom

Ianniello, J.P. (1977). Tidally induced residual currents and salinity in estuaries of constant

breadth and depth. J. Mar. Res., 35:755 – 786.

Imberger, J. and Patterson, J.C. (1990) Physical Limnology. Adv. Appl. Mech., 27:303-475

Janzen, C.D., Wong, K-C. (1998). On the Low-Frequency Transport Processes in a Shallow

Coastal Lagoon. Estuaries., 21:754-766

Jones, M.V. and West, R.J. (2005) Spatial and temporal variability of seagrass fishes in

intermittently closed and open coastal lakes in southeastern Australia. Estuar. Coast.

Shelf. Sci., 2-3: 277-288

Kjerfve, B. and Magill, K.E. (1989). Geographic and Hydrodynamic characteristics of shallow

coastal lagoons. Mar. Geol., 88:187-199.

Kjerfve, B. (1994). Coastal lagoon processes. In Coastal lagoon processes, chapter 1,

(Kjerfev, B. Ed) Amsterdam, New York, Elsevier

Krause, G., and radok, R. (1976). Long waves on the Southern Ocean. In ‘Waves on Water

of Variable Depth’. (Provis, D.G. and Radok, R., Eds) Springer-Verlag: Berlin.

Kurup, G.R., Hamilton, D.P., Patterson, J.C., (1998). Modelling the effect of seasonal flow

variations on the position of salt wedge in a micro tidal estuary. Estuar. Coast. Shelf Sci.,

47:191-208


Largier, J.L., Slinger, J.H., Taljaard, S., (1990). The stratified hydrodynamic of the Palmiet – a

prototypical bar-built estuary. In: Prandle, D., (Eds.), Dynamics and Exchanges in

Estuaries and the Coastal Zone, Coastal and Estuarine Studies, 40, American

Geophysical Union, Washington D.C.

Laval, B. and Imberger, J. (2003). Mass transport between a semi-enclosed basin and the

ocean: Maracaibo System J. Geophys. Res., 108(C7): 3234.

Lewis, R. (1997). Dispersion in estuaries and coastal waters. John Wiley, New York, 312 pp

Lucas, L.V., Cloern, J.E., Koseff, J.R., Monismith, S.G., Thompson, J.K. (1998). Does the

Sverdrup critical depth model explain bloom dynamics in estuaries? J. Mar. Res., 56: 375

– 415

Lugg, A. (1996). Artifical opening of intermittently –opening estuarine lagoons. Technical

paper no. 10A. in the proceedings of the NSW Coastal Conference, 12th -14th November,

Ulladulla, N.S.W. Australia.

Luketina, D. (1998). Simple tidal prism models revisited. Estuar. Coast. Shelf Sci., 46 : 77-84

Lund-Hansen, L.C., Skyum, P., Christiansen, C., (1996). Modes of Stratification in a Semi-

enclosed Bay at the North Sea-Baltic Sea Transition. Estuar. Coast. Shelf Sci., 42, 45-54.

Mann, K.H., Lazier, J.R.N., (1996). Dynamics of Marine Ecosystems: Biological – Physical

Interactions in the Oceans. 2nd Edition. Blackwell Science 394 pp

Masselink, G. and Hughes, M.G. (2003). Introduction to Coastal Processes &

Geomorphology. Hodder Arnold.

Mathieu, P.P., Deleersnijder, E., Cushman-Roisin, B., Beckers, J.M., Bolding, K. (2002). The

role of topography in small well mixed bays, with application to the lagoon of Mururoa.

Cont. Shelf. Res., 22: 1379-1395


Mclean, E.J. and Hinwood, J.B. (1999). The Impact of a Major storm event on entrance

conditions of four NSW south coast estuaries. In the conference proceedings: Coasts and

Ports, Challenges and Directions for the New Century, 14-16th April, Perth, W.A.

Middleton, J.H. (1995). State of the Marine Report for Australia: The marine environment.

Technical Annex 1. Compiled by Zann LP, Ocean Rescue 2000 Program, Department of

the Environment, Sport and territories, Canberra.

Monsen, N.E., Cloern, J.E., Lucas, L.V. (2002). A comment on the use of flushing time,

residence time, and age as transport time scales. Notes in Limnol. Oceanogr. 47:1545 –

1553

Nunes Vaz R.A., Lennon, G.W., de Silva Samarasinghe, J.R. (1989). The Negative Role of

Turbulence in Estuarine Mass Transport. Estuar. Coast. Shelf Sci. 28: 361-377

O’Callaghan, J. (2005). Tidal and Sediment Dynamics of a Partially Mixed, micro-tidal

estuary. PhD Thesis, University of Western Australia, Australia.

Paraso.M.C. and Valle-Levinson.A. (1996) Meteorological Influences on Sea Level and Water

Temperature in the Lower Chesapeake Bay. 1992. Estuaries., 19: 548-561

Pollard, D.A. (1994). Opening regimes and salinity characteristics of intermittently opening

and permanently open coastal lagoons on the south coast of New South Wales. Wetlands

(Australia) 13: 16-35

Provis, D.G. and Radok, R. (1979). Sea – Level Oscillations along the Australian Coast. Aust.

J. Mar. Fresh. Res. 30: 295-301

Pugh, D. (2004). Changing Sea Levels: effects of tides, weather and climate. Cambridge

University Press

Ranasinghe, R. and Pattiaratchi, C., (1999). Circulation and mixing characteristics of a

seasonally open tidal inlet: a field study. Aust. J. Mar. Fresh. Res. 50: 281-90


Restrepo, J.D. and Kjerfve, B. (2002). The San Juan Delta, Colombia: tides, circulations, and

salt dispersion. Cont. Shelf. Res. 22:1249-1267

Rippeth, T.P. and Simpson, J.H. (1996). The frequency and duration of episodes of complete

vertical mixing in the Clyde Sea. Cont. Shelf. Res., 16:933-947.

Rissik, D. Druery, B. Hall, T. and Druery, C. (2003). Determining flushing times for

sustainable estuary management. 12th Annual N.S.W. Coastal conference Surging Ahead:

Success stories in Coastal Management. Port Macquarie, Australia, 4-7th November, 2003.

Robson, B.J. and Hamilton, D.P. (2004). Three-dimensional modelling of a Microcystis

bloom event in the Swan River estuary, Western Australia. Ecol. Modelling. 174:203-222

Romero, J.R., Antenucci, J.P., Imberger, J. (2004). One- and three-dimensional

biogeochemical simulations of two differing reservoirs. Ecol. Modelling, 174:143-160

Roy, P.S., Williams, R.J., Jones, A.R., Yassini, I., Gibbs, P.J., Coates, B., West, R.J., Scanes,

P.R., Hudson, J.P., Nichol, S. (2001). Structure and function of south – east Australian

estuaries. Estuar. Coast. Shelf Sci., 53:351 – 384.

Roy, P.S. (1984). New South Wales estuaries – their origin and evolution. In ‘Developments

in Coastal Geomorphology in Australia’ (Thom, B.G., Ed) Academic press, New York,

pp 99-121

Rubin, H. and Atkinson, J. (2001). Environmental Fluid Mechanics. Marcel Dekker Inc. 728

pp

Rydberg, L. and Wickbom, L. (1996) Tidal choking and Bed Friction in Negombo Lagoon,

Sri Lanka. Estuaries., 19:540-547

Scanes, P., Coade, G., Potts, J. (2002). Load ‘em up? Linking loads of nutrients from

catchments to ecological outcomes in coastal lakes, Coast to Coast: Source to Sea

Conference, 4-8th November 2002, Tweed Heads, NSW, Australia


Simpson, J.H., Brown, J., Matthews, J., Allen, G. (1990). Tidal Straining, Density currents,

and Stirring in the control of Estuarine Stratification. Estuaries. 13:125-132.

Simpson, J.H., Vennell, R. and Souza, A.J. (2001) The Salt Fluxes in a Tidally Energetic

Estuary. Estuar. Coast. Shelf Sci., 52:131-142

Smith, N.P. (2001). Seasonal Scale Transport Patterns in a Multi-inlet Coastal Lagoon.

Estuar. Coast. Shelf Sci., 52:15-28

Smith, N.P. (1993). Tidal and non-tidal flushing of Florida’s Indian River Lagoon. Estuaries.,

16:739-746

Spooner, D. and Spigel, B. (2005). Coastal lake sediments do breathe, and freshwater inflows

can be suffocating. In the NSW Coastal Conference, Narooma, 8-11th Novemner, 2005

Stauble, D. K. (1993). An Overview of Southeast Florida Inlet Morphodynamics. Journal

of Coastal Research., Special Issue No. 18: 1-28.

Stocker, R. and Imberger, J. (2003) Horizontal transport and dispersion in the surface layer of

a medium size lake. Limnol. Oceanogr., 48: 971-982

Suzuki, M.S., Ovalle, A.R.C., Pereira, E.A. (1998). Effects of sand bar openings on some

limnological variables in a hypertrophic tropical coastal lagoon of Brazil. Hydrobiologia.,

368:111-122

Uncles, R.J. (2002). Estuarine physical processes research: some recent studies and progress.

Estuar. Coast. Shelf Sci., 55:829-856

Valle-Levinson, A., Delgado, J.A. and Atkinson, L.P. (2001) Reversing Water Exchange

Patterns at the Entrance to a Semiarid Coastal Lagoon. Estuar. Coast. Shelf Sci., 53:825-

838


Webb, McKeown & Associates. (1998). Smiths Lake: Estuary Processes Study, for the Great

Lakes Council, N.S.W. Australia. Webb, McKeown and Associates Pty Ltd, Sydney,

N.S.W. Australia. 75 pp

Webster, I.T. and Harris, G.P. (2004). Anthropogenic impacts on the ecosystem of coastal

lagoons: modelling fundamental biogeochemical processes and management

implications, Aust. J. Mar. Freshwater Res., 55: 67-78

Wikramanaike N. and Pattiaratchi C.B. (1999). Seasonal changes in a tidal inlet located in a

monsoon regime. Proc Coastal Sediments’99. ASCE, 1462-1477.

Wilson, J., Evans, P. and Kelleher, N. (2002). Fish kills in Cockrone Lagoon – implications

for entrance opening of coastal lakes. Coast to Coast 2002 Conference 4-8th November,

Twin Towns Services Club, Tweed Heads, N.S.W. Australia.

Wolanksi, E., Boorman, L.A., Chicaro, L., Langlois-Saliou, E., Lara, R., Plater, A.J., Uncles,

R.J. and Zalewski, M. (2004). Ecohydrology as a new tool for sustainable management of

estuaries and coastal waters. Wetlands Ecology and Management, 12:235-276

Wong, K-C. (1991). The effect of coastal sea level forcing on Indian River Bay and Rehoboth

Bay, Delaware. Estuar. Coast. Shelf Sci., 32: 213-229

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