Initial Recommendations Regarding the Potential for Nutrient

Impairment of Ecosystem Health in Suisun Marsh, CA

A Report for the San Francisco Regional Water Quality Control Board (Region II)

Agreement Number 12-135-250

12 June 2015

Prepared By Alexander E. Parker1, Matthew C. Ferner2 and Elena Ceballos2 1 The California Maritime Academy, CSU 200 Maritime Academy Drive, Vallejo, CA 94590 2 San Francisco Bay National Estuarine Research Reserve, 3152 Paradise Drive, Tiburon CA 94920

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Cover Figure: Heat maps of water quality data for Suisun Marsh from 2008 to 2015, collected in Second Mallard Slough as part of the San Francisco Bay National Estuarine Research Reserve System-wide Monitoring Program at the Rush Ranch Open Space Preserve. Data presented are mean daily values for (from top to bottom): water temperature, salinity, dissolved oxygen, and turbidity. Data are available at: http://nerrsdata.org

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Contents List of Figures ............................................................................................................................................ - 6 - List of Tables ............................................................................................................................................. - 8 - Introduction ............................................................................................................................................... - 9 -

Estuaries and Tidal Wetlands: Nutrients and Ecosystem Response ..................................................... - 9 - Nutrients in the Northern San Francisco Estuary: Regional Context.................................................. - 12 - A Role for Nutrients in Ecosystem Impairments in Suisun Marsh? ................................................... - 15 -

Nutrient Numeric Endpoints Approach .................................................................................................. - 19 - Nutrient Impairment Indicators for the San Francisco Estuary .......................................................... - 20 - Developing Nutrient Impairment Indicators for Suisun Marsh .......................................................... - 21 -

Pelagic Chlorophyll-a Concentrations ............................................................................................ - 23 -

Dissolved Oxygen Concentrations .................................................................................................. - 25 -

Development of Conceptual Models of Nutrient Impairment for Suisun Marsh .................................... - 26 - Hydrologic Considerations for Nutrient Impairment Conceptual Models for Suisun Marsh ............. - 27 -

Freshwater Inputs From Tributaries, Wastewater and Storm Water Inputs .................................... - 27 -

Tidal Exchange ............................................................................................................................... - 27 -

Water Residence Time .................................................................................................................... - 28 -

Vertical Stratification ...................................................................................................................... - 29 -

Water Clarity and Sediment Supply ................................................................................................ - 29 -

Habitat Types ...................................................................................................................................... - 30 - Nutrient Conceptual Models ............................................................................................................... - 31 -

Nitrogen Conceptual Model for Suisun Marsh ............................................................................... - 32 -

Phosphorus Conceptual Model for Suisun Marsh ........................................................................... - 37 -

Conceptual Models of Proposed Nutrient Impairment Indicators ...................................................... - 40 - Chlorophyll-a (pelagic and benthic) Concentration ........................................................................ - 40 -

Dissolved Oxygen Concentrations .................................................................................................. - 42 -

Current Knowledge of Nutrients and Related Parameters in Suisun Marsh ........................................... - 45 - Previous Analysis of Nutrients in Western Suisun Marsh (Boynton, Peytonia and Sheldrake Sloughs) .. - 45 - New Insights into Nutrients in Suisun Marsh ..................................................................................... - 46 -

Nutrient Discharge from the Fairfield Suisun Sanitation District Outfall in Boynton Slough ....... - 47 -

Nutrient Monitoring by the San Francisco Bay National Estuarine Research Reserve .................. - 52 -

Broad Spatial Sampling of Nutrient Concentrations and Related Water Quality Parameters in Suisun Marsh from 2007-2008 ................................................................................................................... - 78 -

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Nutrient Data from the Moyle Laboratory, UC Davis .................................................................... - 81 -

Initial Conclusions and Recommendations ............................................................................................. - 81 - Lack of Evidence for Nutrient impairment of Ecosystem Health in Suisun Marsh ........................ - 84 -

Initial Recommendations for Monitoring of Indicators of Potential Nutrient Impairment in Suisun Marsh .............................................................................................................................................. - 85 -

References ............................................................................................................................................... - 89 - Appendix I: Additional Indicators of Nutrient Impairment and Conceptual Models for Suisun Marsh.... - 98 -

Benthic Chlorophyll-a Concentrations ............................................................................................ - 98 -

Submerged and Floating Aquatic Vegetation / Macroalgae ........................................................... - 98 -

Conceptual Model of Nutrients and Submerged / Floating Aquatic Vegetation and Macroalgae .. - 99 -

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List of Figures Figure 1: Map of locations with Suisun Marsh sloughs sampled for nutrients and chlorophyll-a during 2007 and 2008…………………………………………………………………..………-16-

Figure 2: Conceptual model for nitrogen in Suisun Marsh habitats…………………………...-33-

Figure 3: Conceptual model for phosphorus in Suisun Marsh habitats………………………..-38-

Figure 4:Conceptual model for microalgal biomass (chl-a indicator) in Suisun Marsh habitats…………………………………………………………………………………………-41-

Figure 5: Conceptual model of dissolved oxygen indicator in Suisun Marsh habitats………...-43-

Figure 6: Mean monthly effluent discharge data from the Fairfield Suisun Sanitation District outfall between January 2008 to November2014 and for the above average water year in 2011………………………………………………………………………………………….....-48-

Figure 7: Annual contributions of NO3, NH4 and organic nitrogen to the total nitrogen loadings from the Fairfield Suisun Sanitation District (FSSD) outfall from January 2008 to November 2014…………………………………………………………………………………………….-50-

Figure 8: Meteorological data collected for Suisun Marsh between January 2008 through December 2015…………………………………………………………………………...……-56-.

Figure 9 : Water quality data collected from First Mallard and Second Mallard Sloughs between January 2008 and December 2014……………………………………………………….……-57-

Figure 10: Mean monthly dissolved inorganic nitrogen concentrations measured at First and Second Mallard Sloughs between May 2008 and January 2015…………………………….…-59-

Figure 11: Mean monthly concentrations of phosphate and silicate collected between May 2008 and December 2014, and chlorophyll-a measured between January 2009 and December 2014……………………………………...……………………………………………………..-60-

Figure 12: Frequency distribution of chlorophyll-a concentrations measured in First and Second Mallard Sloughs………….. ………………………………...…………………………………-64-

Figure 13: Box and whisker plots of seasonal inorganic nitrogen concentrations at First and Second Mallard Slough …………………………………………………….………………….-66-

Figure 14: Box and whisker plots of seasonal inorganic nutrients….…………………………-68-

Figure 15: Box and whisker plots of seasonal chlorophyll-a and phaeophytin concentrations at First and Second Mallard Slough)………… …………………………...…………………….-69-

Figure 16: Mean seasonal dissolved inorganic nitrogen concentrations in First and Second Mallard Sloughs from 2008 to 2014…………………………… .……………………………-70-

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Figure 17: Mean seasonal concentrations of PO4and Si(OH)4 in First and Second Mallard Sloughs from 2008 to 2014. ………………………………………………………………..…-72-

Figure 18: Mean seasonal concentrations of chlorophyll-a and phaeophytin in First and Second Mallard Sloughs from 2008 to 2014……..………………………..…………………………..-73-

Figure 19: Relationship between chlorophyll-a or NO3versus precipitation over the previous three days , previous seven days and previous 14 days for samples collected at First Mallard Slough………………..…………………………………………………………………………-74-

Figure 20: Relationship between NH4 concentration versus precipitation over the previous three days, seven days, and 14 days for samples collected at First Mallard and Second Mallard Sloughs…………………………………………………………………………………………-75-

Figure 21: Chlorophyll-a, nitrate, and phosphate concentrations versus dissolved oxygen percent saturation at First Mallard Slough and Second Mallard Sloughs………………...……-77-

Figure 22: Inorganic nutrient and chlorophyll-a concentrations in sloughs of Suisun Marsh during 2007-2008……………………………………………………...……………………….-79-

Figure 23: Nutrients in Suisun Marsh (mg L-1) prepared by John Durand, UC Davis…..…….-82-

Figure 24: Suggestive evidence for a source of nutrients from the initial overtopping of the marsh plain during a high spring tide in May 2014………………………………...…………………-83-

Figure 25: Conceptual model of submerged and floating aquatic vegetation / macroalgae in Suisun Marsh habitats…………..…………………………………………………………….-100-

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List of Tables Table 1: Listing of numeric nutrient endpoint and Suisun Marsh reports that were reviewed for this report……………………………………...………………………………………………..-17-

Table 2: List of beneficial uses of Suisun Marsh, CA…………………………………..……..-22-

Table 3: Recommended list of nutrient impairment indicators for Suisun Marsh………..……-24-

Table 4: Fairfield Suisun Sanitation District near-field nutrient concentrations for total N, total ammonia and total phosphorus…………………………………………………………………-51-

Table 5: Mean (and range) concentrations of inorganic nutrients at First and Second Mallard Sloughs..........…………………………………………………………………………………..-61-

Table 6: Fraction of nitrogen form for total dissolved inorganic nitrogen at First and Second Mallard Sloughs………………………………….…………………………………………….-62-

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Introduction

Estuaries and Tidal Wetlands: Nutrients and Ecosystem Response

Estuaries worldwide have experienced increases in nutrient loads and concentrations over

the past century, a result of human (anthropogenic) industrialization. Much of this impact has

been driven by increases in human populations adjacent to the coast as well as large-scale

industrial agriculture (Carpenter et al. 1998). In some estuarine systems (e.g., the San Francisco

Estuary; Jassby 2008), industrial and municipal wastewater inputs into estuaries may represent

the largest nutrient source, whereas in other systems, agricultural may represent the largest inputs

of nutrients (e.g., Delaware and Maryland Inland Bays (Glibert et al. 2001); Neuse River Estuary

(e.g., Paerl et al. 1998); Elkhorn Slough (Hughes et al. 2013; 2015).

Stemming from decades-long study of nutrient loading in coastal and estuarine systems,

the impact of nutrient loading to estuaries are known to occupy a broad spectrum of response

(Cloern 1996; 2001; Sharp 2001), from depressed rates of primary production (e.g.,

oligotrophication, Nixon 1990; Dugdale et al. 2013) and resilience to nutrient loading (i.e.,

asymptomatic of enrichment; Cloern 2001; Sharp 2001) to increases in primary production

resulting in highly visible phytoplankton blooms, bottom water anoxia and/or the proliferation of

harmful algal blooms (Boesch 2001). The large variation in ecosystem response reflects variation

in other system-specific ecosystem attributes such as water depth to photic zone depth ratio,

water residence time, intensity and duration of water column stratification, and pelagic and

benthic biological communities, to name a few. Although generalized predictions of ecosystem

responses to nutrient loading are unlikely, the supply of nutrients from anthropogenic sources

likely results in changes to biogeochemical cycles in all systems that have faced such

perturbations and these changes ultimately lead to alteration in coastal and estuarine ecosystem

function (Bricker et al. 2007).

Anthropogenic nutrient loads and concentrations are often associated with “cultural

eutrophication”. Eutrophication refers to changes in trophic state of an ecosystem, where

oligotrophy refers to systems with low organic matter production and eutrophy refers to systems

with high organic matter production. Eutrophication therefore refers to increasing the trophic

state of a system towards eutrophy. Although coastal marine systems, including tidal wetlands,

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are generally naturally eutrophic in large part due to the natural supply and availability of

nitrogen and phosphorus, cultural eutrophication refers specifically to a shift towards eutrophy

due to human disturbance (e.g., nutrient loading) that in turn supports excess algal biomass. This

state shift typically is accompanied by poor consumption of the excess phytoplankton by the

estuarine food web (i.e., inefficient trophic transfer) and ultimately bottom water anoxia fueled

by intense microbial activity (Bricker 2007).

The problem of anthropogenic nutrients in coastal and estuarine systems is generally

restricted to concerns over nitrogen and phosphorus. However, silicon (in the form of silicate,

Si(OH)4) is also considered an important macronutrient in these systems as it is required for

growth by a major functional group of phytoplankton, the diatoms. Still, relative to nitrogen and

phosphorus, the biogeochemical cycle of silicon has been less altered by anthropogenic activity

and so is less commonly associated with increased industrialization. Even with most attention

paid to nitrogen and phosphorus cycling in tidal wetlands, the cycling of silicon in these systems

is an area of limited and needed research (Struyft and Conley 2009).

Tidal wetlands have long been recognized for their ability to assimilate inorganic

nutrients (i.e., act as a nutrient “sink”) and serve as a “source” for organic matter to adjacent

estuarine systems (Odum 1968; Valiela et al. 1978; Nixon 1980; Olsen 1992). This “Outwelling

Hypothesis” has been tested by more than 40 years of research attempting to quantify the relative

importance of tidal marshes in mitigating anthropogenic nutrient loads via uptake and

assimilation by phytoplankton and emergent vegetation (Childers et al. 2000). Relatively few

studies have been able to directly address the Outwelling Hypothesis due to a host of

experimental challenges inherent in attempting to quantify constituent exchange between tidal

wetlands and their adjacent estuaries (Childers et al. 2000), yet the current consensus is that there

is potential for wetlands to serve in this capacity. Similarly, few tidal wetland restoration

programs have quantitatively assessed restoration trajectories for nutrients, thereby

demonstrating improvements in water quality (Zedler and Callaway 1999). The ability of

specific tidal wetlands to assimilate nutrients appears to be driven in part by their water retention

times (Woltermade 2000). Based on the paradigm of wetlands as a nutrient sink, the use of

managed wetlands is common to address issues of water quality and nutrient loading

downstream of industrial and municipal wastewater discharges. The loss of wetlands due to

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human population pressure, accounting for roughly half of wetland loss in recent decades (Dahl

and Johnson 1991; Chambers et al. 1999), could exacerbate nutrient loading to estuaries and the

coastal ocean by removing a potentially important sink for excessive nutrient loads.

Although much emphasis has been placed on understanding the potential that wetlands

serve to mitigate nutrient loads (i.e., the Outwelling Hypothesis), substantially less effort has

been made to specifically address questions of whether nutrients to adversely affect wetland

structure and function (Olson 1992; Moshiri 1993; Kadlec and Knight 1996). Nonetheless, tidal

wetland habitats are undoubtedly altered by excessive nutrients (Ryther and Dunstan 1971) in

ways that could undermine wetland integrity (Venterik et al. 2002; Zedler and Kircher 2005;

Deegan et al. 2012) and influence the potential of wetlands to respond to and mitigate climate

change (Kirwan and Megonigal 2013).

The potential for nutrient impairment of tidal wetlands may be most profound in the

subtidal slough habitats that serve as conduits for nutrients, organic matter and other materials

(Siegel et al. 2011). Elevated nutrients, combined with climate forcing (Hughes et al. 2015),

longer water residence times that are typical in sinuous tidal sloughs (along with associated

differences in the physical environment, including elevated water temperatures and calm,

shallow water conditions) may promote large accumulations of pelagic phytoplankton biomass

and classical cultural eutrophication. Nitrogen and phosphorus enrichment may stimulate both

pelagic and benthic phytoplankton (microphytobenthos); nitrogen has been shown to

disproportionately stimulate microphytobenthos whereas phosphorus may promote pelagic

phytoplankton (by inhibiting benthic forms; Zhang et al. 2014). Microphytobenthos community

composition and abundance have been used for the assessment of ecosystem health and

impairment, including impairment from excessive nutrient loads in lake systems and in European

rivers (Tan et al. 2012; Almeida et al. 2014). In the tidal wetland systems of Yaquina Bay, OR,

Hankin et al. (2012) experimentally linked decreased benthic diatom species richness to nitrogen

concentrations.

Although the response of tidal wetlands to elevated nutrients may be observed in open

water habitats, it has also been suggested that nutrients impact emergent vegetation in tidal

wetlands (Chambers et al. 1999). Specifically, excessive nutrients are thought to alter soil

nitrogen-to-phosphorus (N:P) ratios and change the competitive relationships between plant

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species (Zedler and Kircher 2005; Wang et al. 2014). For example, Deegan et al. (2012),

working in Plum Island Estuary, MA, showed reductions in below ground biomass, resulting in

loss of emergent vegetation, suggesting that the ability of tidal wetlands to assimilate nutrients

might be exceeded, also seen in east coast marshes with shifts from Spartina alterniflora to

Distichlis spp.(Fox et al. 2012). The introduction of upland wetland species including

Phragmites spp. along the U.S. East Coast and along the Gulf of Mexico coast has been

hypothesized to have been exacerbated by increases in nutrients that release Phragmites from

limitation and allow it to outcompete other species (Levine et al. 1991; Meyerson et al. 1998).

Nutrient enrichment experiments in wetlands have revealed a broad spectrum in responses that

can lead to either increased or decreased rates of accretion of organic matter, thereby affecting

how tidal wetlands respond to sea level rise (Kirwan and Megonigal 2013).

The abundance of macrophytes and macroalgae in tidal wetland sloughs may be yet

another indicator of nutrient impairment of tidal wetland habitats (Fong et al. 1998; McGlathery

2001; McKee et al. 2011). Associated with intertidal, shallow (<10m) subtidal, and tidally muted

environments (McKee et al. 2011), dense macroalgal cover is often associated with

eutrophication in the saline portions of estuarine habitats (Fong et al. 1993; Sutula et al. 2011)

and some effort has been made to develop quantitative benchmarks for macroalgal abundance

and nutrient impairment in southern California estuarine waters (Green et al. (2014). Freshwater

macrophytes, including the San Francisco Delta invader, Brazilian waterweed, Egeria densa, are

shown to respond to ammonium and phosphorus availability in their native range (Feijoo et al.

1996; 2002). The increased bioavailability of macroalgal biomass (Valiela et al. 1997) means

that it will more readily enter the estuarine food web and drive higher rates of microbial

respiration thus imparting strong influence on dissolved oxygen concentrations and be associated

with hypoxia events. Within the freshwater Delta, submerged and aquatic vegetation, including

Egeria densa and water hyacinth (Eichhornia crassipes), has become a management issue.

Nutrients in the Northern San Francisco Estuary: Regional Context

The San Francisco Estuary (SFE) is the largest estuary on the U.S. West Coast and, with

the cities of San Francisco, Oakland and San Jose along its shores, is highly urbanized. Often

described as two separate estuarine systems, the SFE includes: 1) the South Bay that extends

south from the San Francisco – Oakland Bay Bridge; and 2) the northern SFE that includes the

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sub-embayments of Central, San Pablo and Suisun Bays, as well as tidally influenced reaches of

the Sacramento-San Joaquin Delta. The distinction in these systems is made mainly by

hydrology. The South Bay lacks a major freshwater source and is thus characterized as a lagoon-

type system with relatively long water residence time. In contrast, the northern SFE has two

major river systems, the Sacramento and San Joaquin Rivers that converge in the Delta near the

eastern end of Suisun Bay. The Sacramento River supplies much of the freshwater flow to the

northern SFE, and due to seasonal variation in those flows, the residence time of water in the

northern SFE is seasonally and inter-annually variable. Temporal and spatial differences in

freshwater flow and water residence time within the SFE have important implications for the

nutrient loads and concentrations as well as for the potential for nutrient impairments.

Nutrients are supplied to the northern SFE through anthropogenic loading (i.e., municipal

wastewater treatment plants [WWTPs] from the inland cities of Stockton and Sacramento, and

from agriculture in the Central Valley) and as natural inputs from the watershed and the Pacific

Ocean. The SFE watershed drains approximately 40% of California’s land surface area and tidal

exchange with the Pacific Ocean through the Golden Gate is vigorous, with approximately 25%

of the tidal prism being exchanged on each tide (Conomos et al. 1985). Jassby (2008) estimated

that roughly 90% of the ammonium (one form of inorganic nitrogen) that enters the northern

SFE is derived from secondary level treatment WWTPs on the Sacramento River and delivered

to the northern SFE via river flow. Elevated concentrations of nitrate (a second form of nitrogen)

are supplied by advanced secondary treatment WWTPs within the northern SFE, including on

the San Joaquin River at Stockton. As a result of these inputs, nutrient concentrations in the SFE

and Delta are relatively high, exceeding concentrations found in many other US estuaries that

suffer from nutrient impairment via cultural eutrophication and excess phytoplankton blooms

(Cloern and Jassby 2012).

The regional paradigm after many decades of study in the SFE is that nutrients are not

central to the control of phytoplankton biomass, and therefore the current potential for nutrient

impairment is low relative to other estuarine systems (Cloern 2001). For example, the original

nutrient Basin Plan suggested that only limited nutrient management was necessary to be

protective of ecosystem health in the region (Feger et al. 2012). Instead of nutrients, it is

generally assumed that phytoplankton primary production rates are controlled principally by the

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availability of light (Cole and Cloern 1984), which is strongly attenuated in the SFE by high

loads of suspended sediment (e.g., Cole and Cloern 1984; 1987). Additionally, the lack of

phytoplankton blooms is primarily due to intense benthic grazing, most notably by the invasive

Asian Overbite Clam, Potamocorbula amurensis (Alpine and Cloern 1992; Kimmerer and

Thompson 2014). The establishment of the clam in the mid-1980s apparently eliminated

summertime accumulations of phytoplankton that occurred in Suisun Bay (Alpine and Cloern

1992). Accumulation of phytoplankton biomass (i.e., a phytoplankton “bloom”) is now rare in

the northern SFE, and average phytoplankton biomass occurs at low concentrations that have

been shown to limit growth of higher trophic levels (<10 µg L-1 chlorophyll-a; Muller-Solger et

al. 2002).

Over the past decade there has been renewed interest in the potential that nutrients may

play a role in shaping ecosystem structure and evidence that the system may be losing some

resilience to nutrient enrichment. In the South Bay there is evidence that P. amurensis densities

were reduced in the late 1990s, allowing phytoplankton biomass to increase there (Cloern et al.

2007; Senn et al. 2013). In the northern SFE, improved water clarity (Schoellhamer 2009) has

been implicated in increases in the abundance of phytoplankton despite continued success of P.

amurensis (Jassby 2008; Kimmerer and Thompson 2014). Recently, there is growing

appreciation for the potential that nutrients may play a regulatory role in phytoplankton

physiology, even at non-limiting concentrations, with harmful algal bloom (HAB) species

abundance and algal toxins being proposed as an indicator of nutrient impairment for the San

Francisco Bay (Senn et al. 2013). Indeed, the estuary and Delta do experience HABs (Cloern et

al. 2005; Herndon and Cochlan 2008; Lehman et al. 2005; 2008; Lee et al. 2015). As a result,

efforts are now underway to better characterize the potential for nutrient impairment throughout

the SFE and Delta.

One area of research has highlighted the potential importance of the separate

considerations of the forms of nitrogen (i.e., nitrate and ammonium) that comprise the dissolved

inorganic nitrogen (DIN) pool; historically, all forms of inorganic nitrogen were lumped into this

single pool for consideration of impacts to primary producers (Parker 2005). Nitrate and

ammonium may play a synergistic role with water clarity, water residence time (Wilkerson et al.

2006; Dugdale et al. 2013; Glibert et al. 2014), and clam grazing (Dugdale et al. unpublished) in

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the development of phytoplankton blooms in the SFE. A primary mechanism in which

anthropogenic nutrient loads have influenced phytoplankton is through ammonium inhibition of

phytoplankton nitrate uptake. In the SFE the nitrate pool is much larger than the ammonium pool

and some phytoplankton (i.e., some diatoms) may assimilate nitrate faster than ammonium

allowing for more rapid growth. In fact, Siegel et al. (2010), suggest that wetland habitats like

Suisun Marsh have the potential to reduce ammonium concentrations (primarily through

nitrification) thereby serving as a sink for anthropogenic ammonium loads, and mitigating

ammonium inhibition of diatoms.

A Role for Nutrients in Ecosystem Impairments in Suisun Marsh?

The brackish wetlands extending upslope from Suisun Bay comprise an important

component of the SFE known as Suisun Marsh, the largest contiguous estuarine marsh on the

west coast of North America (Fig. 1). Suisun Marsh contains a diverse community of emergent

vegetation and associated fauna, including many rare and endangered terrestrial and aquatic

species, and is an important stop for thousands of birds migrating on the Pacific Flyway. The

productive marsh ecosystem also supports a variety of recreational and sportsman activities; the

majority of the wetlands have been diked and managed for hunting of waterfowl. These managed

areas are periodically reconnected to remnant tidal wetlands and Suisun Bay through a network

of water control structures and natural tidal sloughs.

Decades of water and wetland management, scientific study and regional planning have

yielded many reports and environmental assessments of Suisun Marsh with a recurring focus on

various aspects of regional water quality (Table 1). Tidal habitats within Suisun Marsh are

influenced primarily by freshwater outflow from the Delta and saline water from the Pacific

Ocean, but also receive local inputs of freshwater through discharge from the Fairfield Suisun

Sanitation District WWTP, runoff from surrounding agricultural and grazing lands, and runoff

from the municipalities of Fairfield and Suisun City. However perhaps even more significant in

altering the historical patterns of habitat, hydrology and water quality in Suisun Marsh is the

seasonal filling and draining of the more than 50,000 acres of diked wetlands managed as duck

hunting clubs. Since 1879, these wetland areas have been managed to reduce the extent of tidal

influence and lower water salinity in order to select for freshwater plant species attractive to

waterfowl (Moyle 2014). The practice of holding and releasing water in support of duck club

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Table 1: Listing of numeric nutrient endpoint and Suisun Marsh reports that were reviewed for this report.

Topic Area Citation Description Numeric Nutrient Endpoints

Sutula et al. 2013. A review of scientific approaches supporting NNE assessment framework development for San Francisco Bay. San Francisco Regional Water Quality Control Board Basin Planning and TMDL Unit

Discussion of numeric nutrient endpoint implementation for the San Francisco Estuary

Sutula et al. 2011 Review of indicators for Development of nutrient numeric endpoints in California Estuaries. Technical Report 646

Discussion of numeric nutrient endpoint implementation for California.

San Francisco Bay

Senn and Novick 2013. San Francisco Bay Nutrient Conceptual Models

Provides conceptual models for nitrogen, phosphorus and their interaction with phytoplankton biomass, dissolved oxygen, phytoplankton community composition and algal toxins.

Senn et al. Suisun Bay nutrients Parallel effort to NNE investigating nutrient – phytoplankton interactions in Suisun Bay.

McKee et al. 2011 Numeric nutrient endpoint development for the San Francisco Bay Estuary; Literature review and Data gaps analysis Technical Report 644

A description of the NNE framework approach for application to the SFE and identification of data gaps and challenges in NNE application to the SFE

Suisun Marsh Siegel et al. 2011 Final Evaluation Memorandum: strategies for resolving low dissolved oxygen and methylmercury events in northern Suisun Marsh. Project number 06-283-552-0

Analysis of dissolved oxygen sags in western Suisun Marsh sloughs. Points to vegetation management approaches in managed wetlands as principle source of BOD.

Tetra Tech, Inc. 2013 Suisun Marsh Conceptual Model/ Impairment Assessment Report for Organic Enrichment, Dissolved Oxygen, Mercury, salinity and nutrients.

Initial analysis of nutrients in western Suisun Marsh, including characterizing stream and watershed loadings, FSSD loadings and historical analysis of nutrients

Siegel et al. Suisun Marsh Physical and Aquatic Habitat models

Mueller-Solger and Bergamaschi, 2005 Conceptual Model: Organic Matter in Suisun Marsh.

Generalized conceptual models of organic matter sources and sinks along marsh plain.

Baginska 2012. Suisun Marsh TMDL for Methylmercury, dissolved oxygen and nutrient biostimulation

Project definition and plan to develop a TMDL to address water quality impairments in Suisun Marsh

Finfrock et al. 2001 Comprehensive review Suisun Marsh Monitoring Data 1985- 1995.

Historical context of water quality monitoring program in Suisun Marsh

O’Rear & Moyle 2013. Trends in Fish and Invertebrate Populations of Suisun Marsh (annual reports)

UC Davis Suisun Marsh Fish Study: monthly water quality and fish abundance data

SCCWRP 2014. Science Supporting Dissolved Oxygen Objectives for Suisun Marsh (Technical Report 830)

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management can lead to seasonal reductions in dissolved oxygen concentrations in the

surrounding tidal sloughs, directly affecting fish habitat and at times leading to localized fish

kills. Even fully tidal “reference sites” within the marsh, such as First Mallard and Second

Mallard Sloughs, have experienced dissolved oxygen concentrations below 2 mg L-1 (NERRS

2015), which is the generally accepted hypoxic threshold and increasingly found in estuaries

(Kennish 2002). It is not clear if reductions in dissolved oxygen concentrations in Suisun Marsh

tidal sloughs are natural or anthropogenic, but in those areas where subtidal pockets of restricted

circulation may be common it is likely that many organisms are able to escape or tolerate short-

term periods of hypoxia (Senn et al. 2013). Less attention has been paid to drivers of nutrient

enrichment itself or the consequences of such enrichment, but in addition to direct runoff and

WWTP discharge, the supply of nutrients to Suisun Marsh may be enhanced by draining of the

duck clubs and associated increases in organic matter load (Siegel et al. 2010) in aerobic activity

(e.g., Koerselman et al. 1993).

The large scale alteration of tidal wetland habitats and ubiquitous nutrient enrichment of

estuarine systems worldwide limit access to true reference sites, including within the SFE

(Moyle 2014), however, tidal wetlands are naturally active areas for organic matter production,

much of it originating from tidal and super tidal emergent vegetation (Muller-Solger and

Bergamaschi 2005) and may exhibit some dissolved oxygen depletion as a result. The traditional

view of nutrient-driven hypoxia has been applied to Suisun Marsh which is listed as impaired by

nutrients under 303d of the Clean Water Act (SFBRWQCB 2007), despite a lack of clear links

between nutrients and the resulting hypoxic events. The Suisun Marsh Conceptual Model report

(2011) includes a chapter on nutrients in Suisun Marsh including a summary of nutrient load

estimates and some analysis of historic and present nutrient concentrations within northwestern

Suisun Marsh. The report also provides a conceptual model for nutrient impairment of Suisun

Marsh ecosystem health through the production of phytoplankton biomass and subsequent

dissolved oxygen depletion (their Figure 6.1). Siegel et al. 2011 reported that much of the

biochemical oxygen demand associated with hypoxic conditions in the northwestern Suisun

Marsh is due to organic matter from the management of emergent vegetation within duck clubs

with less emphasis placed on the potential for excessive algal production fed by anthropogenic

nutrients. Within this report we provide conceptual models and explore existing data to shed

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light on the potential role that anthropogenic nutrients play in ecosystem health impairments of

Suisun Marsh.

Nutrient Numeric Endpoints Approach

Given that nutrients may lead to impairment of ecosystem health in tidal wetlands it is

instructive to consider the specific ecological pathways by which nutrients would be likely to

lead to impairment in these environments. As described by others (e.g., McKee et al. 2011,

Sutula et al. 2013; Senn et al. 2013), although elevated water-column nutrients may signal the

potential for impairment to a water body, it is generally not possible to show impairment based

solely on elevated nutrient concentrations. The result is that elevated nutrients are themselves

likely to be a poor indicator of nutrient impairment. Instead, one must develop a set of potential

negative outcomes that can be directly tied to elevated nutrients; these outcomes then serve to

link nutrient concentrations with ecosystem impairments.

The nutrient numeric endpoint (NNE) approach is a framework for guiding aquatic

nutrient management based upon a set of identified key ecosystem responses to nutrient

enrichment, as well as indicators of these ecosystem responses. The objective is to set numeric

indicator thresholds, or endpoints, which allow natural resource management agencies to

translate narrative water quality objectives into quantitative threshold values. Specifically (Sutula

et al. 2013):

i) The NNE framework allows for quantitative guidance to translate narrative water

quality objectives through specific numeric threshold values of key attributes of a

water body.

ii) The NNE framework defines key nutrient response indicators and establishes numeric

endpoints for these indicators based on the ecological response of a water body to

nutrient over-enrichment.

In the section that follows, we provide guidance on anticipated ecosystem responses to elevated

nutrients in Suisun Marsh and a set of potential indicators of these responses that could fit into a

nutrient monitoring program. First we provide context for NNE applications in the broader

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region: the SFE. Next we provide a rationale for selecting specific nutrient indicators for

application in Suisun Marsh. Finally we provide conceptual models that link elevated nutrient

concentrations to indicators through ecosystem responses in several habitats within the marsh. In

this section we will not provide quantitative guidance on threshold values for the proposed

indicators as data in support of such quantitative targets is currently lacking for Suisun Marsh. In

the Current Knowledge section we explore the existing data on nutrient concentrations and

indicators (i.e., pelagic chlorophyll-a and dissolved oxygen concentrations) and provide

examples of how quantitative thresholds may be developed in future efforts. In the Initial

Conclusions section, we provide guidance on development of monitoring programs that may aid

in developing future quantitative guidance for nutrients in Suisun Marsh.

Nutrient Impairment Indicators for the San Francisco Estuary

The San Francisco Bay Regional Water Quality Control Board (SFBRWQCB) is using

the NNE framework to guide development of separate nutrient management strategies for the

SFE (e.g., Senn et al. 2013). The purpose of developing a separate NNE framework for Suisun

Marsh is to determine appropriate impairment indicator variables for this complex marsh

ecosystem, with its distinct hydrology and management history. Several helpful planning

documents have been developed either directly as part of the process of developing a general

NNE framework for the SFE or to support other parallel efforts for the State of California (Table

1). We have used these reports as the basis for selecting potential indicator and response

variables that may be reasonably applied to a nutrient management strategy for Suisun Marsh.

Where appropriate, we considered the potential for selecting indicators and responses that were

consistent with those selected by the San Francisco Estuary Nutrient Management Strategy team

(Senn et al. 2013) for application in Suisun Marsh. Such alignment is not always reasonable, but

for those indicators that are shared between these efforts, there is the potential for synergy in

future data sharing and analysis.

McKee et al. (2011) articulated four attributes of robust indicators of nutrient impairment

of the SFE to serve as guidance for development of NNEs, and all of these attributes are

applicable to Suisun Marsh. The attributes place emphasis on direct links between nutrient

impairment and ecosystem (primarily hydrologic) drivers and they stress the importance of

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selecting endpoints that can be reasonably incorporated into routine ecosystem monitoring

programs using robust and accessible methodologies. The attributes are paraphrased here:

1. Indicators should have well-documented links to beneficial uses of the estuary.

2. Indicators should have predictive relationships with nutrient and hydrologic

drivers.

3. Indicators should have scientifically sound and practical measurement

approaches.

4. Indicators must be able to show a trend towards increasing or decreasing

impairment of beneficial uses due to nutrients.

Based on this guidance, Senn et al. (2013) identified and proposed four indicators of

nutrient impairment for the subtidal habitats of the SFE (excluding Suisun Marsh): 1)

phytoplankton biomass (as chlorophyll-a), 2) dissolved oxygen concentrations, 3) phytoplankton

community composition, and 4) algal toxin concentrations.

Both chlorophyll-a and dissolved oxygen concentrations may be good candidate

indicators for nutrient impairment in Suisun Marsh and at least some long term data exist for

each of these indicators in some regions of Suisun Marsh. We are not aware of any studies that

characterize phytoplankton community composition in Suisun Marsh, and given the relatively

high cost to implement a monitoring program for phytoplankton community composition, we

eliminated that indicator for the purposes of this report (but see recommendations section).

Similarly, the lack of knowledge about the presence of algal toxins in Suisun Marsh leaves its

utility as an indicator of nutrient impairment in this system completely unknown and only

speculative at this time (but see recommendations section).

Developing Nutrient Impairment Indicators for Suisun Marsh

Beneficial uses of Suisun Marsh mirror broadly accepted benefits of tidal wetlands and

are provide in Table 2. Based upon potential indicators of nutrient impairment described by

McKee et al. (2011), Sutula et al. (2013) and Senn et al. (2013), we selected 1) pelagic

chlorophyll-a concentrations, 2) benthic chlorophyll-a concentrations, 3) dissolved oxygen

concentrations, and 4) submerged aquatic vegetation / macroalgal cover as potential indicators of

- 22 -

Table 2: List of beneficial uses of Suisun Marsh, CA

Foraging and nesting habitat for resident species of plants and animals,

Includes fish, mammals, reptiles and amphibians. Some marsh species are endemic to Suisun Marsh, for example the Suisun Song Sparrow and Suisun Thistle, and many are protected under state or federal law as threatened or endangered species, such as the California Least Tern, Ridgway’s Rail (formerly California Clapper Rail), and California Black Rail (Moyle at al. 2014).

Wintering habitat for migratory waterfowl

Utilize both managed duck clubs as well as natural tidal sloughs, creeks, and vegetated marsh areas.

Protection from storm surge and flooding,

Includes that associated with sea level rise.

Long-term storage of nutrients, contaminants and carbon

Due to the reduced rate of decomposition of organic matter under anaerobic conditions (Reddy and DeLaune, 2008).

Public open space for recreation, including hunting, fishing, boating and wildlife viewing

Tidal wetland restoration projects,

Such as those tied to mitigation actions, employment opportunities, and property tax revenue as specified in the Suisun Marsh Habitat Preservation and Restoration Plan (Suisun Marsh Plan, 2014).

Scientific research In support of resource conservation and management, such as studies on drivers and responses of potential indicators of ecosystem health and the potential for water quality impairment

- 23 -

nutrient impairment of Suisun Marsh (Table 3). These four indicators fit the criteria established

by McKee et al. (2011). Because of the lack of information on benthic chlorophyll-a and

submerged aquatic vegetation / macroalgae in Suisun Marsh we provide a rationale and

conceptual model for these indicators in the recommendation section at the end of report. Below

we describe briefly the rationale used to select the remaining indicators of nutrient impairment

for Suisun Marsh but stress that simply investigating nutrient impairment based on pelagic

chlorophyll-a and dissolved oxygen (because these data are readily available) may leave an

incomplete understanding of nutrient impairment of ecosystem health. The collection of ancillary

data, including meteorological conditions, water temperature, conductivity, salinity, and some

proxies of water clarity (e.g., turbidity, optical backscatter or Secchi disk depth, concentrations

of suspended solids) are necessary to make links between nutrients and impairment response.

Pelagic Chlorophyll-a Concentrations

Pelagic chlorophyll-a concentration serves as a proxy of phytoplankton biomass and is an

important indicator of nutrient impairment, meeting each of the criteria set out by McKee et al.

(2011). Phytoplankton biomass is most closely tied to eutrophic and culturally eutrophic systems,

quite literally representing a large fraction of organic matter production in culturally eutrophic

systems. Elevated chlorophyll-a can impair beneficial uses by releasing unpleasant odors,

reducing aesthetics (impacting Beneficial Use: Recreation) and increasing biochemical oxygen

demand (BOD), which can lead to hypoxic or even anoxic conditions (Beneficial Use: Foraging

and nesting habitat). Measurement of chlorophyll-a concentrations is routine with well-

established methods (e.g., Arar and Collins, 1996) and is generally comparable across

laboratories and monitoring programs. Interpretation of chlorophyll-a concentrations as an

indicator of nutrient impairment must include consideration of the severity of events (e.g.,

magnitude of elevation in chlorophyll-a concentrations), the duration of elevated chlorophyll-a

events, and their spatial extent. Because measurements of chlorophyll-a are routine, estimates

can be compared across time and space within systems as well as across different systems; the

selection of pelagic chlorophyll-a concentrations as an indicator of nutrient impairment allows

for synergy between a potential future Suisun Marsh nutrient impairment program with the

ongoing effort in the greater SFE. Long term data on nutrients and pelagic chlorophyll-a

- 24 -

Table 3: Recommended list of nutrient impairment indicators for Suisun Marsh. List is based upon the analysis of McKee et al. 2011 and adoption by Senn et al. 2013 and Sutula et al. 2013. Descriptions of habitats types are provided in Development of Conceptual Models section of this report. Nutrient impairment indicators in bold are indicators where there is data for analysis of impairment effect. Italicized indicators lack data.

Habitat types Nutrient Impairment

Indicator

Subtidal Slough

(>2m) habitats • Pelagic Chl-a

• Dissolved oxygen

• SAV / macroalgae

Intertidal slough

habitats

• Benthic chl-a

• SAV / Macroalgae

Upper Intertidal

habitats

• Pelagic Chl-a

• SAV / Macroalgae

Managed wetlands

(Duck clubs)

• Pelagic Chl-a

• Dissolved oxygen

• SAV / macroalgae

- 25 -

concentrations do exist for a limited spatial extent of Suisun Marsh allowing for at least some

initial analysis of the potential for nutrient impairments based on this indicator.

Dissolved Oxygen Concentrations

Dissolved oxygen concentrations are often used as an indicator of cultural eutrophication

and nutrient loading, and like pelagic chlorophyll-a concentration, dissolved oxygen

concentration is a nutrient impairment indicator selected by the SFE NNE (Senn et al. 2013),

thus allowing for synergy between the related nutrient management efforts in Suisun Marsh and

the SFE. The link between nutrient inputs and changes in water column dissolved oxygen

concentrations occurs via aerobic decomposition of the organic matter supported by

anthropogenic nutrient loading, but cultural eutrophication typically requires multiple drivers

including large scale climate forcing, nutrient loads, ample light, poor flushing rates / trophic

transfer, and water column stratification. The impact of low dissolved oxygen on beneficial uses

is the potential disruption to microbial populations and biogeochemical cycling that may be

manifested as negative changes in water quality, including discoloration and release of

unpleasant odor. Hypoxia and anoxia can negatively impact natural communities of invertebrates

and fish where these conditions occur both at lethal and sub-lethal levels; for fish this may

reduce overall habitat or disrupt migration. Dissolved oxygen concentrations can be quantified in

the laboratory by titration (EPA Method 360.2; EPA 1972) but are more commonly measured in

the field by handheld sondes or optical luminescent-based technology. Field-measurement

approaches require regular maintenance and calibration of sensors but allow for rapid, real-time

measurements. After the initial investment in instrumentation, large amounts of data can be

collected at relatively low cost and directly compared across monitoring programs.

Biochemical oxygen demand may be estimated from carbon content of organic matter

and an assumed respiratory quotient (moles of oxygen consumed equaling moles of carbon

respired; may be assumed as 1:1). Low dissolved oxygen concentrations (i.e., hypoxia

conditions) occur primarily during the summer when water bodies experience thermal

stratification and bottom waters become isolated, restricting oxygenation at the air-water

interface. There are examples from many estuaries and coastal ocean areas that suffer from

bottom-water hypoxia including in the Chesapeake Bay and the well-known “Dead Zone” within

the Gulf of Mexico. With the exceptions of the deep water ship channel in the San Joaquin River

- 26 -

at Stockton (Lehman et al. 2004), South Bay sloughs (associated with South Bay Salt Pond

Restoration Project, David Senn, pers. comm.) and western Suisun Marsh (Siegel et al. 2011),

waters of the SFE generally do not suffer from hypoxic or anoxic conditions. Currently, the SF

Bay NERR monitors dissolved oxygen concentrations in two sloughs in western Suisun Marsh

and various targeted research programs also may be monitoring dissolved oxygen concentrations

in certain locations.

Development of Conceptual Models of Nutrient Impairment for Suisun Marsh

Conceptual models of nutrient interactions with ecosystem health are central to the

development of an NNE framework. Because the focus of such a framework is on indicator

endpoints and not nutrient concentration endpoints, explicitly stated models of the linkages

between nutrient loadings, ecosystem responses to nutrient loadings, and ecosystem indicators of

those responses are critical for making predictions and testing hypotheses about how nutrients

may impair ecosystem health within Suisun Marsh.

A series of nutrient conceptual models was developed by Senn et al. (2013) that: 1)

separately describe the major pools and fluxes of nitrogen and phosphorus, and 2) describe the

interactions of nutrients with defined impairment indicator endpoints of phytoplankton biomass,

phytoplankton composition, dissolved oxygen concentration and algal toxins. We modified the

nutrient conceptual models and the models for phytoplankton and dissolved oxygen for use in

four main habitat types within Suisun Marsh described below. Like Senn et al. (2013), we first

present the conceptual models for Suisun Marsh nutrients that include explanations of: 1) the

nutrient forms that occur, 2) the sources of nutrients and their forms, and 3) the processes

involved in their cycling in the marsh environment. In the Initial Conclusions section we develop

potential conceptual models for two additional nutrient impairment indicators:

microphytobenthos and SAV/macroalgae.

The conceptual models take into consideration hydrologic conditions within Suisun

Marsh that act as master variables in driving ecosystem processes. We also divide Suisun Marsh

into four habitat types that are qualitatively delineated by where they sit in the tidal frame and/ or

the amount of time that they are inundated by water. Thus, linkages between habitat types are

assumed to be driven in large part by variations in hydrology. The four habitat types are: 1)

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managed wetlands (duck clubs), 2) upper intertidal habitats (wetted only on spring high tides), 3)

lower intertidal habitats (slough walls and low marsh inundated and exposed to the atmosphere

twice daily), and 4) subtidal sloughs.

Hydrologic Considerations for Nutrient Impairment Conceptual Models for Suisun Marsh

The conceptual models of nutrient impairment require consideration of several

hydrologic processes that occur within Suisun Marsh, including external nutrient loading (which

is the product of water flow and nutrient concentration), water residence time, tidal processes

(which vary on daily, lunar, annual and decadal time scales), and water column mixing and

vertical stratification. These processes influence both nutrient concentrations within Suisun

Marsh and the time scale for nutrient – habitat interactions. Hydrologic linkages among the four

habitat types that we defined are not well constrained, limiting application of these conceptual

models as a single unified system. Consequently, investigation of water and nutrient exchange

between habitats represents a high priority area for future research.

Freshwater Inputs From Tributaries, Wastewater and Storm Water Inputs

There are several potential anthropogenic and natural external nutrient loads to Suisun

Marsh through external freshwater inputs. The primary anthropogenic point source of nutrient

loading into Suisun Marsh is the Fairfield Suisun Sanitation District (FSSD) WWTP, a publicly

operated treatment plant that discharges between 10 and 18 million gallons of treated municipal

waste each day to western Suisun Marsh (primarily into Boynton Slough; see Siegel et al. 2011).

The FSSD WWTP discharges phosphorus and nitrogen, primarily in the form of nitrate.

Additionally, anthropogenic nutrient sources in Suisun Marsh include runoff from grazing and

agricultural lands, the Potrero Hills Landfill (although water treatment of these sources occurs on

site; Barbara Baginska, pers. comm.), the marina at Suisun City and Delta outflow. We are

unaware of studies that attempt to quantify these anthropogenic loads (Siegel et al. 2011).

Tidal Exchange

Tidal exchange is the dominant mixing process is Suisun Marsh. The SFE experiences

mixed semidiurnal tides, with twice daily high and low tides of differing levels, biweekly spring-

neap tidal cycles than can introduce about 0.5m variation in tide heights, quarterly height

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variations associated with the solstices and equinoxes, and an 18.6-year tidal “epoch” cycle

reflecting a range of gravitational forces. The highest tide ranges occur during the summer and

winter solstices. Winter Delta outflow raises high tides and cuts off low tides, dampening tide

range and raising tide levels. Suisun Marsh spring tide range is approximately 1.2 to 1.6 meters

depending on location in the region. Suisun Slough and Montezuma Slough are the main

conduits of tides in and out of the system, with variation in tidal magnitude and exact timing

throughout the network of smaller sloughs and creeks that bisect the Marsh off of these two

major sloughs. The natural tidal marsh plains (such as Rush Ranch) are at fairly high elevations

and thus receive tidal inundation only during higher spring tides. Many of the tidal marshes that

formed outboard of constructed levees are at lower elevations and are inundated more frequently.

Tidal exchange between the diked managed wetlands ad tidal sloughs are a function of water

control structure operations and relative wetlands elevations and thus ability to gravity drain and

flood versus use of pumps to drain

Because nutrient loading is a function of nutrient concentration and the volume of water

begin exchanged, non-point nutrient loads from the SFE to Suisun Marsh might exceed the

primary point source from the FSSD WWTP if the exchange of water between the Delta or

Suisun Bay and Suisun Marsh is high even if the concentrations of nutrients coming from the

Delta are much lower than FSSD effluent discharge. Nutrient loading from seasonal streams are

likely much smaller than from the FSSD WWTP but may be significant on a seasonal basis,

especially in the immediate receiving waters (Siegel et al. 2011).

Water Residence Time

Water residence time within Suisun Marsh habitats varies across habitat types, location

within the Marsh, and seasonally. Residence time in the tidal sloughs is a function of proximity

to the tidal source, the bathymetry of the sloughs, seasonal operations of the diked managed

wetlands, and seasonal operations of the Montezuma Slough Salinity Control Structure. Sloughs

with a more proximal connection to Suisun and Grizzly bays via Suisun and Montezuma Sloughs

are likely to have lower water residence times than more distal sloughs (Fig 1). In contrast,

sloughs farther upstream from Montezuma and Suisun Sloughs and the upper ends of long

sloughs are likely to have longer water residence times, such as the Nurse-Denverton Slough

area, Peytonia and Boynton sloughs in the northwest Marsh and Cordelia Slough in the west

- 29 -

Marsh. Seasonal diked managed wetlands operations can extract substantial water volumes from

the tidal sloughs, resulting in increased slough residence times. Operations of the Montezuma

Slough Salinity Control Structure can increase residence times in the northeast Marsh. Water

residence time within the duck clubs is quite predictable, as are the time periods of discharge

from those managed wetlands (e.g., Seigel et al. 2011).

Vertical Stratification

Drivers that influence whether or not vertical stratification occurs in Suisun Marsh

aquatic habitats are wind, tidal mixing, temperature (thermoclines), salinity (haloclines), and

water depth. Winds have a strong seasonal signal, with summer winds being typically stronger,

longer in duration, frequent, and westerly/northwesterly. Winter winds tend to be storm

associated, more southerly, potentially large in magnitude but generally short in duration. Tidal

mixing acts to keep the water column from stratifying. Only where significant local freshwater

inflows occur are haloclines able to form, such as Boynton Slough with the FSSD discharge. The

Montezuma Slough Salinity Control Structure may induce haloclines in Montezuma Slough as

its intent is to move Delta freshwater flows into Montezuma Slough. Subtidal tidal sloughs with

long residence times that are wind sheltered, such as around the margins of Suisun Marsh, have a

comparatively greater stratification potential than do the well-mixed larger sloughs subject to

winds. Thermoclines have the potential to establish in the peripheral sloughs during the summer

and fall when air temperatures are warm, though light winds in fall are more likely to facilitate

thermoclines. The shallow waters in diked managed wetlands have some stratification potential

due to thermal heating. As they are commonly flooded in the fall for hunting season when winds

tend to be light and air temperatures can get quite warm, stratification would be most likely to

occur in the fall. We are unaware of studies that examine water column stratification within

Boynton Slough near the FSSD effluent discharge.

Water Clarity and Sediment Supply

Water column sediment concentrations affect the depth of the photic zone and thus

phytoplankton uptake of nutrients. Sediment sources to Suisun Marsh waters are the local

watershed, Delta, San Pablo Bay, and local re-suspension. In general, the highest water column

sediment concentrations are from Delta outflow (Suisun Bay) and local wind and current driven

- 30 -

re-suspension in shallow bays (Grizzly Bay, Honker Bay, and Little Honker Bay). Local

watersheds can yield sediment pulses during winter storms. Sediment concentrations diminish in

Montezuma and Suisun sloughs due to deposition as flood tides move upstream and the limits of

tidal excursion up these sloughs. Stratification could limit re-suspension.

Habitat Types

As described above, we separated Suisun Marsh conceptually into four habitat types for

consideration of potential nutrient impairments and indicator responses. A brief description of

these four habitat types follows. Although open water areas of Suisun Marsh are restricted to the

managed wetland and subtidal slough habitats , the interactions between nutrients and the marsh

plain, including both upper intertidal (inundated only on spring high tides) and lower intertidal

habitats (inundated on daily tides) likely represent important pathways for nutrient

transformations and the potential for impairment of ecosystem health.

Managed wetlands (a.k.a., duck clubs) occupy roughly 210 km2 of the 470 km2 total area

of Suisun Marsh (Moyle et al. 2014). These wetlands are managed by periodic flood and drain

cycles using 300 gated culverts, in an effort to support the growth of preferred vegetation of

waterfowl by reducing salinity. The managed ponds are filled (typically to depth of about 0.3 m)

with low salinity water from the Delta in September and October in advance of hunting season,

which runs from mid-October through mid-January. Ponds then are drained when hunting season

concludes in January. From that time until March the ponds are repeatedly filled and drained in

order to remove excess salt from the sediments within the ponds (Moyle et al. 2014).

Upper intertidal habitats are wetted only periodically during spring high tides. During

these periods, water moves out of the sloughs onto the vegetated soils of the marsh plain where it

can interact with rooted plants and benthic microalgae. Water may pool upon the marsh plain,

evaporate, or percolate through marsh soils and return to the tidal creeks and sloughs. These

overtopping events represent an opportunity for nutrients to be added to the marsh plain,

potentially fueling future growth of emergent plants (i.e., organic matter production), and also

may act to export organic matter from the marsh plain into the subtidal sloughs where it could

increase local biochemical oxygen demand.

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Lower intertidal habitats are wetted approximately twice daily within the marsh due to

inundation by mixed semidiurnal tides. These habitats include extensive tracts of tule and other

low-elevation plants lining the tidal sloughs throughout the marsh, but much of the lower

intertidal habitat within Suisun Marsh is restricted to unvegetated, muddy banks of sloughs and

small creeks. Although the biochemical processes in these habitats are not well characterized in

Suisun Marsh, they likely support a rich microphytobenthos (Cohen et al. 2014), including

benthic diatoms and prokaryotic microorganisms that can play a consequential role in mediating

nutrient transformations and fluxes (Cornwell et al. 2014).

Subtidal portions of the sloughs represent a series of interconnected and tidally driven

pelagic habitats within Suisun Marsh. Some of these sloughs (e.g., Suisun Slough and

Montezuma Slough) are relatively deep (often greater than 2-3 m at low tide) whereas other

sloughs may lose the majority of their water volume on the outgoing tide. Subtidal slough

habitats serve as receiving water for managed wetland discharge, the effluent discharge from the

FSSD WWTP, as well as water from the adjacent Grizzly Bay (Suisun Bay; via Suisun Slough)

and the Delta (via Montezuma Slough) (Fig.1).

Nutrient Conceptual Models

Borrowing the rationale provided by Senn et al. (2013), only nitrogen and phosphorus

conceptual models were considered for evaluating Suisun Marsh nutrient impairment. Nitrogen

and phosphorus loading, concentration and cycling are more susceptible to anthropogenic

alteration than are other nutrients; therefore, if nutrient impairment is identified for Suisun

Marsh, there is the highest potential for positive ecosystem responses to nutrient management of

nitrogen and phosphorus. The macronutrient silicate is important for microbial biogeochemistry

in the SFE as it is essential for growth of diatoms, which are central phytoplankton in the SFE as

described above. Silicate is supplied to the system primarily through the weathering of silicate-

rich rock in the Sierras and as a result, silicate concentrations are generally very high in the SFE

(>200 μmol L-1, 5.6 mg Si L-1; Wilkerson et al. 2006), well in excess of elemental requirements

by diatoms relative to either nitrogen or phosphorus.

We describe the nutrient forms, sources and key cycling (biogeochemical processes) for

nitrogen and phosphorus. Discussion of nutrient forms is based on basic aquatic

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biogeochemistry. Nutrient sources are based on information from comparable systems and,

where available, we characterize nutrient sources specifically for Suisun Marsh. Similarly,

anticipated rates of nutrient transformation processes were collected from the literature on

comparable systems or, where available, from information on wetlands of the SFE, including

Suisun Marsh. Limited information on recent nutrient concentrations within Suisun Marsh also is

provided in the section that follows.

Nitrogen Conceptual Model for Suisun Marsh

Nitrogen Forms

The aquatic nitrogen (N) cycle is complex because N is found in several forms (i.e.,

redox states from -3 to +5) and is tightly cycled through several important microbially-mediated

processes including assimilation, ammonification (regeneration), nitrification, assimilatory ,

dissimilatory nitrate reduction (denitrification) and nitrogen fixation (Fig. 2). Forms of N found

in aquatic systems include dissolved inorganic nitrogen (DIN) comprised of nitrate (NO3; redox

state of +5), nitrite (NO2; redox state of +3), and ammonium (NH4; redox state of -3). Dissolved

organic nitrogen (DON; operationally defined as the fraction of organic N that passes through a

GF/F filter with a nominal pore size of 0.7-μm; Sharp et al. 2004) includes dissolved free and

combined amino acids (generally measured as “bulk DON”) as well as urea (CH4N2O). Urea is

often considered with the DIN as it is sometimes used in fertilizers and has increased

substantially in some culturally eutrophic estuaries (Glibert et al. 2006), but it does not appear to

represent a substantial fraction of the DIN in the SFE (Wilkerson et al. 2006; Blaser et al. 2013;

Parker, unpublished data). Nitrogen is also found as particulate organic nitrogen (PON;

operationally defined as the fraction of organic N that is retained on a filter with a nominal pore

size of 0.7-μm), either as autotrophic (phytoplankton), heterotrophic (bacterial) or detrital

(decaying) PON. Atmospheric N (dinitrogen; N2) is the largest pool of N on Earth, but much of

this form of N is unavailable for biogeochemical cycling except via N2 fixation. Nitrogen

fixation rates are poorly constrained for the SFE, and N2 is considered to be of limited

importance within open water habitats but may be significant within wetland habitats such as

Suisun Marsh (Yorty 2005). Similarly, the importance of PON and DON in N biogeochemistry

of the SFE is poorly understood (Senn et al. 2013) but concentrations of these forms of N are

likely elevated and therefore may represent a relatively large pool of N within Suisun Marsh.

- 33 -

- 34 -

Nitrogen Sources (Loading)

Although poorly characterized, there are several natural N sources to Suisun Marsh

including N2 fixation, atmospheric deposition, diffuse watershed sources such as soil and

terrestrial vegetation leachate, submarine groundwater discharge, small tributaries and ephemeral

streams and exchange between the SFE and Suisun Marsh via Suisun and Montezuma Sloughs.

We are aware of only one study that has investigated N2 fixation rates within SFE wetlands

(Yorty 2005) but literature from other wetland systems suggest variable atmospheric N sources

(Zedler 1982; Langis et al. 1990). Similarly, estimates of N derived from soil and vegetation

leachate, resulting in DIN and DON, are currently unavailable, but based on natural abundance

stable isotope studies (Canuel et al 1995) these sources do contribute at least some fraction of N

to the system. Periodic draining of tidal wetland soils may serve to supply DIN and DON to the

water column. Groundwater nitrogen is known to be significant in some estuaries and tidal

wetlands (e.g., Valiela et al. 1978; see review of New England marshes; Bowen et al. 2007) but

we are unaware of system-specific data on groundwater inputs of N for tidal wetlands in the SF

E, including Suisun Marsh. The Suisun Marsh Conceptual Model Report (2013; Table 1)

summarized (as reported by Davis et al. 2000) potential N loads to Suisun Marsh via the upland

watershed. Nitrogen loads measured in Ledgewood and Suisun Creeks in spring were 4.6 kg N

ha-1 yr-1 and 0.5 kg N ha-1 yr-1, respectively. The Suisun Marsh Conceptual Model Report (2013)

also estimated atmospheric N deposition as wet loadings of 2.45 kg N ha-1 yr-1 or 315.5 kg d-1 to

Suisun Marsh and Dry load of 210.5 kg d-1 to Suisun Marsh.

Nitrogen loading from FSSD represents a significant source of anthropogenic nutrients to

western Suisun Marsh. The FSSD employs advanced secondary wastewater treatment that

includes nitrification; this results in an effluent N load mostly in the form of NO3. The Suisun

Marsh Conceptual Model Report provided estimates of typical N loading based on data from

2012 to 2014) of 1.332kg N d-1 We have collected FSSD loading data for both N and P between

2008 and 2014 which will be summarized in the “Current Knowledge” section that follows.

A second (and likely less important) anthropogenic nitrogen source is from livestock that

are grazed within the local watershed. This nutrient source to the marsh is poorly understood

and, if it is significant, the potential impact should be constrained to relatively localized areas of

the marsh near to where grazing activity is ongoing, and concentrated during autumn months

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when the rainy season typically commences after a prolonged dry period. In some cases, such as

during dry years at Rush Ranch Open Space Preserve on the western side of the Potrero Hills,

cattle are provided access through the marsh to drinking water in large tidal sloughs. Waste from

cattle entering and adjoining the sloughs may result in locally elevated urea and NH4

concentrations.

Another poorly constrained nitrogen source with the potential influence especially

western Suisun Marsh is storm water runoff from Fairfield and Suisun City. Although generally

considered to be a smaller source than WWTP loading (Senn et al. 2013), storm water runoff

may be important seasonally and in localized settings, especially in smaller receiving waters such

as dead end sloughs. The situation with respect to storm water runoff in Suisun Marsh is unclear

as slough habitats may receive relatively large pulses of nitrogen after storm events, especially if

significant watershed runoff occurs through the Delta, but the wetland habitats themselves may

also serve to intercept local storm water, reducing immediate effects on adjacent slough habitats.

The Potrero Hills Landfill sits within a local watershed that drains into Suisun Marsh and could

in some instances be a potential source for storm water runoff of nutrients and contaminants, but

regulations require rigorous containment and monitoring to ensure negligible impacts of the

landfill on the surrounding water quality (Barbara Baginska, pers. comm.).

Nitrogen Cycling

Nitrogen assimilation is the incorporation of DIN and DON into cellular constituents

(e.g., protein) by primary producers, including pelagic phytoplankton, microphytobenthos, SAV

and emergent vegetation as well as by heterotrophic bacteria (Fig. 2). Nitrogen assimilation has

not been estimated for Suisun Marsh but rates of NO3 uptake for channel habitats for nearby

Suisun Bay range from 0.03 mg N L-1 h-1 in winter to 0.25 mg N L-1 h-1 in spring. NH4 uptake in

Suisun Bay varies between lows of 0.16 mg N L-1 h-1 in winter to 0.45mg L-1 h-1 in spring and

0.52 mg N L-1 h-1 in summer (Wilkerson et al. 2006). It is well established throughout the marine

and aquatic literature (see reviews by Dortch 1990; Collos and Harrison 2014) as well as in the

SFE specifically (Wilkerson et al. 2006; Dugdale et al. 2007; Parker et al. 2012) that NH4

concentrations between 0.014 to 0.056 mg L-1 inhibit phytoplankton uptake of NO3 such that as

long as NH4 concentrations exceed these inhibition thresholds, NO3 behaves conservatively and

is not bioavailable to autotrophs.

- 36 -

Once assimilated, N resides in organisms as autotrophic or (heterotrophic bacterial)

biomass (PON; >0.7-μm) and can then be assimilated by higher trophic levels in the water

column (e.g., zooplankton or fish) or form sinking particles that may be buried in sediments,

consumed by benthic grazers, aerobically respired by bacteria at the sediment surface, or

denitrified in anoxic sediments (see below) (Fig. 2).

Primary producers lose organic N to the DON pool upon cell death, through passive

cellular excretion, and when inefficiently consumed by zooplankton grazers (i.e., sloppy feeding)

(Fig. 2). The DON is then assimilated by heterotrophic bacteria fueling an estuarine microbial

loop (Parker 2005) and the re-mineralization (regenerated) of N to NH4. The microbial loop is

generally not well-characterized for estuaries (but see Parker 2005 and references therein) but is

assumed to be of diminished importance in estuaries relative to marine systems. In contrast, NH4

regeneration within both the water column and underlying sediments may be a substantial

process (Kleckner 2007; Cornwell et al. 2014).

Ammonium undergoes a series of transformations during nitrification (chemosynthesis

carried out by NH4-oxidizing bacteria and archaea both in pelagic (Julian Demashek,

unpublished data) and benthic environments (Mosier and Francis 2008; Damashek et al. 2014)

Fig. 2). The sequential oxidization of NH4 first to NO2 and then to NO3 is generally rapid,

resulting in low NO2 concentrations in aquatic systems. When NO2 is observed it is generally

indicative of the decoupling of nitrification processes or of very high rates of nitrification.

Nitrification couples dynamics of DIN with O2 for oxidation, contributing to BOD.

Denitrifcation is another microbially-mediated N pathway that returns DIN in the form of

NO3 to the atmosphere as N2 (and N2O) gas. The denitrification pathway represents a sink for

DIN from N-enriched estuaries like the SFE. Denitrification is an anaerobic respiratory process

that is common in anoxic areas with high organic matter concentrations such as tidal wetland

soils associated with emergent vegetation. N2 fixation is the conversation of atmospheric

nitrogen into microbial biomass.

- 37 -

Phosphorus Conceptual Model for Suisun Marsh

Phosphorus Forms

Compared with the biogeochemical cycling of nitrogen described above, the phosphorus

(P) cycle is far less complicated as there are fewer P forms of interest (Fig. 3). Inorganic P occurs

as dissolved PO4 and may be measured in a dissolved (<0.7-μm) fraction or complexed with

mineral particles (i.e., sediments, Lebo 1991; especially Iron (III) sediments). The particle-bound

fraction is considered less available for phytoplankton but PO4 readily adsorbs and desorbs from

particle surfaces such that both of the inorganic fractions should be considered within P budgets.

Dissolved (<0.7-μm) and particulate (>0.7-μm) organic phosphorus represent organic P that is

either free or contained within biota.

Phosphorus Sources (Loading)

The sources of phosphorus (P) to aquatic systems generally, and within Suisun Marsh

specifically, are similar to those identified for nitrogen described above. Both natural and

anthropogenic phosphorus sources influence P concentrations within slough habitats of Suisun

Marsh and we can identify potential P loading, but in most cases only limited information for

Suisun Marsh. Because there is no atmospheric source of P there is no exchange with the

atmosphere.

There are several potential natural sources of P to Suisun Marsh. The first of these is P

loading from small ephemeral wet streams and creeks. For example, P loads of 0.02 kg P ha-1 yr-1

0.17 kg P ha-1 yr-1 in Ledgewood and Suisun Creeks, respectively (Tetra Tech, 2013). These

inputs likely vary substantially on seasonal time scales, with enhanced P loading during periods

of increased precipitation and only limited P loading during the dry summer and early autumn

months. Groundwater input of P may also be important but we are unaware of any assessment of

groundwater input of P within Suisun Marsh. A third natural source of P is through leachate from

marsh soils and terrestrial vegetation. The close association of the emergent vegetation, marsh

soils and slough habitats make these loading term potentially large in wetlands, but we are

unaware of quantitative studies for Suisun Marsh. Finally, although P loading from the Delta (via

Montezuma Slough) and Grizzly Bay (via Suisun Slough) may be from anthropogenic sources to

these water bodies, the flux into and out of Suisun Marsh is part

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- 39 -

of natural river flow and tidal exchange and so is considered here as a potentially important

natural source of P to the Marsh.

As described for anthropogenic nitrogen loads, there are several potential anthropogenic

P sources for Suisun Marsh including wastewater treatment plants (i.e., FSSD), animal waste

associated with cattle grazing activities within Suisun Marsh, agricultural activities, and storm

water runoff. Cattle grazing and agricultural phosphorus sources are poorly constrained for

Suisun Marsh. The best constrained of the anthropogenic sources is from the Fairfield Suisun

Sanitation District (FSSD) WWTP. Mean monthly loading from FSSD described below. As

noted by Senn et al 2013, roughly 80% of the total P load from WWTP is as PO4.

Storm water P loading is likely strongly seasonal within the Mediterranean climate, with

high potential for storm water P input during the rainy season (Nov – May) and only limited

input during the summer and autumn. Within small sloughs storm water P input may represent a

large, if ephemeral nutrient source, especially in sloughs with poor flushing and long water

residence time. Although overall within the SFE system storm water nutrients are thought to be

of diminished importance relative to other natural and anthropogenic sources, storm water may

be a relatively important source of P in Suisun Marsh when considered on certain temporal and

spatial scales.

Phosphorus Cycling

Phosphate is assimilated by primary producers and incorporated into particulate organic

phosphorus. Primary producers include pelagic phytoplankton, the microphytobenthos,

submerged aquatic vegetation and emergent vegetation (Fig. 3). Some fraction of the particulate

organic phosphorus is lost to the dissolved organic phosphorus pool through natural excretion.

Similarly when the primary producers die or is consumed, some fraction is lost to the dissolved

organic phosphorus phase, with other particulate organic phosphorus is re-mineralized by

heterotrophic bacteria that release inorganic phosphorus. The dissolved organic phosphorus may

be taken up by primary producers or re-mineralized by bacteria to PO4. Particulate organic

phosphorus and particulate phosphorus may transferred to higher trophic levels or sink to the

sediment surface where it can be re-mineralized or adsorb or desorb from mineral particles to the

PO4 pool.

- 40 -

Conceptual Models of Proposed Nutrient Impairment Indicators

The goal in developing conceptual models for proposed nutrient impairment indicators

are to explicitly link the ecosystem response to nutrients with the observable indicator. Also

explicit in these models are interactions between multiple factors (e.g., importance of water

clarity for phytoplankton N assimilation) whose effects on ecosystem function are integrated into

the system response and observed indicator. We have combined chlorophyll-a indicators (i.e.,

pelagic or phytoplankton biomass and benthic or microphytobenthos biomass) in a single

conceptual model which is presented first, followed by the dissolved oxygen conceptual model

and submerged aquatic vegetation and macroalgae.

Chlorophyll-a (pelagic and benthic) Concentration

For efficiency, conceptual model for chlorophyll-a is presented here for both pelagic

(water-column) and benthic microalgae (microphytobenthos) (Fig. 4). We are unaware of any

available data for microphytobenthos in Suisun Marsh, so analysis of current knowledge is

restricted to pelagic chlorophyll-a. A brief discussion of the potential use of benthic chlorophyll-

a as an indicator for nutrient impairment will be discussed in the Conclusions and

Recommendations section that appears at the end of this report.

Chlorophyll-a is a common proxy for pelagic and benthic microalgae. The abundance and

production of pelagic and benthic microalgae are common indicators of ecosystem health in

marine and aquatic systems and are used in many systems for this purpose (see review by Cloern

et al. 2014). Microalgae form the base of the estuarine food web and despite the potential for

abundant terrestrial and wetland-derived (i.e., allochthonous) particulate and dissolved organic

matter, organic matter derived from microalgae appears to be more bioavailable within the SFE

(Jassby et al. 2002; Sobczak et al. 2002, 2005).

Microalgal production is dependent upon nutrient supply such that nutrients potentially

play a bottom-up control on their abundance (Fig. 4). Nitrogen and phosphorus uptake by

phytoplankton is assumed to occur at fixed ratios set by phytoplankton N and P cellular

requirements. The ratio most commonly applied is the Redfield ratio of 16 : 1 for nitrogen to

phosphorus although this ratio is variable across phytoplankton taxa and dynamic within species.

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- 42 -

In addition to nutrient availability, phytoplankton biomass production is dependent upon the

amount of solar irradiance that phytoplankton are exposed to. Solar irradiance reaching the water

or marsh plain surface varies seasonally and daily with cloud cover and wind-driven re-

suspension of sediments (Schoellhamer et al. 2003). Irradiance that does reach the marsh is

further modified by water column suspended sediment concentrations, water column mixing and

the ratio of water column depth and euphotic zone depth. If microalgal blooms reach sufficient

density, they may contribute to declines in water clarity. Because of high suspended sediment

concentrations and generally low phytoplankton biomass, declines in water clarity due to the

accumulation of algal biomass are not considered to be a current problem in the SFE but this

may not hold for regions within Suisun Marsh.

Microalgal biomass is a function of production rate as well as losses through sinking and

re-suspension, grazing by zooplankton or benthic filter feeders, and physical processes such as

advection. The accumulation of microalgal biomass (i.e., elevated chlorophyll-a) may be due to

poor flushing and / or inefficient trophic transfer rather than elevated primary production rates

driven by high nutrients (Fig. 4).

The link between excess microalgal production and low dissolved oxygen concentration

is through respiration of the resulting microalgal organic carbon (BOD). A simple approach for

estimating the BOD from microalgal production is to calculate phytoplankton carbon biomass

from chlorophyll-a measurements using an assumed carbon-to-chlorophyll-a ratio (mg C : mg

Chl-a); carbon to chlorophyll-a ratios may vary widely (Kimmerer et al. 2012) but are often

assumed to vary between 35 and 50 (Cloern et al. 1995).

Dissolved Oxygen Concentrations

Dissolved oxygen concentrations are controlled by physical (exchange with the

atmosphere across the air – water interface) and biological processes (Fig. 5). Dissolved oxygen

readily exchanges with the atmosphere but the exchange is more rapid in waters that is cold and /

or experiences turbulent mixing from winds and tides. The sloughs of Suisun Marsh may

experience diminished mixing relative to the SFE and so dissolved oxygen may deviate from

equilibrium with the atmosphere. Seasonal variation in the dissolved oxygen concentrations are

observed due to physical processes due to the inverse relationship in oxygen saturation with

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- 44 -

water temperature. Similarly, dissolved oxygen is more soluble in freshwater compared to water

with dissolved solutes (salinity) and so seasonal variation in freshwater flow may influence

dissolved oxygen concentrations through physical processes alone.

The primary biological processes that influence dissolved oxygen concentrations in

Suisun Marsh are primary production, which results in production of dissolved oxygen during

the day and microbial (both autotrophic and heterotrophic) respiration that occurs both during the

day and at night (Fig. 5). Within the sunlight portion of the water column (i.e., the photic zone)

the balance between primary production and respiration generally results in net dissolved oxygen

production, whereas during the night (and below the water column photic zone) the balance

between production and respiration results in net dissolved oxygen consumption. This results in

diel dissolved oxygen cycles with maxima near mid day and minima during predawn hours. The

relationship between photosynthesis that results in the production of dissolved oxygen and

respiration resulting in the consumption of dissolved oxygen can be reasonably constrained by

applying photosynthesis and respiratory quotients (mol O2 produced or consumed per mol C

produced or consumed) of 1.

Aerobic breakdown of accumulated particulate and dissolved organic matter can lead to

dissolved oxygen sags, hypoxia and anoxia (Fig. 5). Although the breakdown of organic matter

happens within the water column, a large fraction of organic matter settles to the benthos where

elevated rates of aerobic decomposition occur. When bottom waters are isolated from the surface

(and therefore physical exchange of dissolved oxygen with the atmosphere is eliminated) net

consumption of dissolved oxygen can occur rapidly leading to ecosystem impairments for

vertebrate and invertebrate species. In tidal marshes emergent vegetation represents a potentially

large source of organic matter to subtidal sloughs. These inputs of allochthonous organic matter

have the potential to drive high rates of aerobic respiration and dissolved oxygen consumption.

Similarly, managed wetlands may serve as “incubators” for microalgal populations that consume

nutrients. When managed wetland waters are drained to the surrounding subtidal habitats, the

organic matter from microalgal biomass represents yet another allochthonous organic matter

source to drive down dissolved oxygen concentrations.

Historically, allochthonous organic matter loading occurred from WWTP effluent but

upgrades to treatment works mandated by the Clean Water Act resulted in substantial decreases

- 45 -

in anthrophonic organic matter loading to estuarine waters. Nitrification of NH4 to NO3 also

consumes dissolved oxygen. Because the major WWTP in Suisun Marsh carries out advanced

secondary treatment (i.e., nitrification of effluent within the WWTP) NH4, the substrate for

nitrification is diminished. Still NH4 is supplied to subtidal habitats of Suisun Marsh through

sources described above and is produced during regeneration (ammonification) of organic matter

to NH4 during aerobic decomposition.

Current Knowledge of Nutrients and Related Parameters in Suisun Marsh

Considering the significance of Suisun Marsh as one of the largest contiguous areas of

tidal wetlands on the West Coast, current nutrient monitoring within wetland sloughs is

surprisingly limited both temporally and spatially (Tetra Tech 2013). The two most consistent

nutrient monitoring programs within Suisun Marsh are the San Francisco Bay National Estuarine

Research Reserve (SF Bay NERR) System-wide Monitoring Program at First Mallard and

Second Mallard Sloughs in the Rush Ranch Open Space Preserve (http://www.nerrsdata.org),

and the near-field compliance monitoring at the FSSD WWTP outfall in Boynton Slough

between 2005 and the present.

Previous Analysis of Nutrients in Western Suisun Marsh (Boynton, Peytonia and Sheldrake Sloughs) The Suisun Marsh Conceptual Model (Tetra Tech 2013) report provided some nutrient

concentration context from historic data collected in Suisun Slough (station S42) between 1978-

1985 by the California Department of Water Resources and contemporary sampling between

2000 and 2011 by FSSD as part of the WWTP permit requirements in the northwestern sloughs

of Suisun Marsh (Boynton, Peytonia and Sheldrake Sloughs; Barbara Baginska, pers. comm.).

Ammonium concentrations during the 1970s – 80s varied between 0 - 0.3 mg N L-1 (0 to 21

µmol L-1 while NO3+NO2 varied between 0 – 0.9 mg L-1 (0 to 65 µmol L-1 ). Total P

concentrations were reported between 0.1 to 0.35 mg P L-1 (3 µmol L-1 to 11 µmol L-1). The

reported water N : P ratio was less than 16:1 (although it is not explicitly stated whether this ratio

is based on molar or gravimetric ratio), suggesting that if N and P were assimilated by

phytoplankton with an average N : P demand of 16: 1 (Redfield 1963), N would be exhausted

before P. Although it is difficult to assess “baseline” conditions for Suisun Marsh (i.e., human

- 46 -

disturbance has been part of the Suisun Marsh since the late 1870s) the nutrient concentrations

above provide an indication of the nutrient environment of Suisun Marsh 30 to 40 years ago.

Samples collected between 2000 and 2011 showed substantially elevated nutrients

compared to the 1970s to 80s averages with N concentrations in Boynton Slough between 0 - 0.4

mg N L-1 (0 to 29 µmol N L-1) for NH4 (an increase of as much as 33%) and 0-18 mg N L-1 ( 0 to

1.24 mmol N L-1) for NO3 (as much as a 20-fold increase) with highest concentrations found at

stations immediately above and below the FSSD effluent discharge pipe. NH4 concentrations

were similar (~ 0.4 mg N L-1) in Peytonia, Sheldrake and Chadbourne Sloughs, with few

exceedances. NO3 concentrations were lower (<2 mg N L-1; 142 µmol N L-1) in these sloughs

compared to Boynton Slough near the outfall. Similarly PO4 was substantially elevated in

Boynton Slough (0.5 to 4 mg P L-1 (16 -129 µmol P L-1) compared to Peytonia Slough (<1 mg P

L-1) and Sheldrake Sloughs (0.0.6 mg P L-1) and contemporary PO4 measurements were

substantially elevated (roughly 11-fold) relative to the 1970-80s record (Tetra Tech 2013). The

elevated N and P in the northwestern Suisun Marsh were attributed to the FSSD discharge into

Boynton Slough (Tetra Tech 2013). These nutrient data analyses completed by Tetra Tech

(2013) provide a background of historical nutrients and characterize the contemporary nutrient

field near where clear ecosystem impairments (i.e., episodic low DO events) have been reported

by Siegel et al (2011).

New Insights into Nutrients in Suisun Marsh We have identified four nutrient data sets that are either publicly available or were

supplied to us by individual investigators for further analysis in the context of the conceptual

models. With the exception of FSSD discharge data (between 2008 and 2015), the data sets that

we worked with were not included in the Tetra Tech report (2013) and so provide new

information on nutrient concentrations in Suisun Marsh. The first of these new data sets is from

the SF Bay NERR – System Wide Monitoring Program in First and Second Mallard Sloughs.

The second new data set was from an 11-month special study conducted between 2007 and 2008

with broad spatial sampling for nutrients in Suisun Marsh that was summarized by Parker and

Cohen (2011). Finally, an excerpt from long-term monthly nutrient monitoring in multiple

sloughs throughout Suisun Marsh was provided by John Durand (UC Davis). Additionally,

- 47 -

datasets that are collected as part of special studies for nutrients and related parameters in Suisun

likely exist, however we were not able to obtain these data for inclusion in this report.

In the section that follows we explore the state of knowledge about nutrient

concentrations, including nitrogen forms (NH4, urea, NO3, and NO2) and PO4; although not

explicitly considered in our nutrient conceptual models, Si(OH)4 trends were also considered

where available in this analysis. We characterize available proposed indicators of nutrient

impairment, including concentrations of pelagic chlorophyll-a, phaeophytin (a degradation

product of chlorophyll-a) and dissolved oxygen. We also characterize several of the synergistic

drivers described in the nutrient conceptual models either explicitly (water column transparency,

water temperature) or implicitly (meteorological data, photosynthetically active radiation) in

order to test hypothesized mechanisms by which nutrients may impair water quality in Suisun

Marsh.

Nutrient Discharge from the Fairfield Suisun Sanitation District Outfall in Boynton Slough

Discharge (liters per day, L d-1) and concentrations for total N, NH4, NO3 and P between

January 2008 and November 2014 were provided by Giti Havarian of the FSSD analytical

laboratory (Figs. 6 and 7). The length of the times series obtained was selected to match the

period of operation of the SF Bay NERR monitoring program in Suisun Marsh (described in

detail below). From these data, nitrogen and phosphorus loading were calculated as:

𝑁𝑁 𝑜𝑜𝑜𝑜 𝑃𝑃 𝑙𝑙𝑜𝑜𝑙𝑙𝑙𝑙𝑙𝑙𝑙𝑙𝑙𝑙 (𝑚𝑚𝑙𝑙 𝑙𝑙−1) = [𝑁𝑁]𝑜𝑜𝑜𝑜 [𝑃𝑃](𝑚𝑚𝑙𝑙𝐿𝐿−1) × 𝑒𝑒𝑒𝑒𝑒𝑒𝑙𝑙𝑒𝑒𝑒𝑒𝑙𝑙𝑒𝑒 𝑙𝑙𝑙𝑙𝑑𝑑𝑑𝑑ℎ𝑙𝑙𝑜𝑜𝑙𝑙𝑒𝑒(𝐿𝐿)

The mean monthly FSSD discharge rate (106 L d-1) between 2008 and 2014 varied

between lows of 39 x 106 L-1 d-1 in August and 70 x 106 L-1 d-1in March (Fig. 6A) The higher

flows observed in Marsh are consistent with precipitation runoff entering the WWTP during the

rainy season and the above average rainfall year in 2011 is also consistent with this. Lower flows

from FSSD in August and September are also consistent with strongly seasonal rainfall patterns

in the region. Mean monthly N concentrations in FSSD discharge varied between 18 mg N L-1 in

February and March and 26 mg N L-1 between August and October (Fig. 6B). The variability in

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- 49 -

N concentration in the discharge also likely reflects regional patterns in precipitation, with storm

water runoff serving to dilute municipal wastewater N resulting in lower N concentrations during

the periods when the region experiences rainfall and higher N concentrations in effluent during

periods with low rainfall. The resulting mean daily N load to Suisun Marsh from FSSD varied

between 970 kg N d-1 to >1250 kg N d-1 with higher N loading in March and lower values in

August through October (Fig. 6C). The higher N loads in March, associated with higher rainfall

suggest that discharge is a larger driver the variation in N loading compared to variation in N

concentrations in the effluent load. Previous estimates of N load from FSSD to Boynton Slough

between 2012 and 2014 (1332 kg N d-1; Tetra Tech 2013) agree well with our analysis. Mean

daily P concentration in FSSD discharge varied between 3 mg P L-1 and >5 mg P L-1, with lower

concentrations in winter and spring and elevated P in fall (Fig. 6D). The mean monthly FSSD P

load varied between 175 kg P d-1 (in September) and 240 mg P d-1 (in March) (Fig. 6E).

Modeling conducted by Tetra Tech (provided by Barbara Baginska in a memo 8 June 2015)

suggest that nutrients from FSSD discharge likely remain elevated within Boynton and Peytonia

Sloughs and persist in elevated concentrations at least to intersection of these sloughs with

Suisun Slough.

The form of N discharged from FSSD was also investigated (Fig. 7). The FSSD reports N

discharge as total N, NO3, and NH4; the difference between total nitrogen and the sum of NO3

and NH4 was assumed to be organic nitrogen. Over the data record from 2008 to 2014 the N

discharge from FSSD was mostly (>94%) in the form of NO3 (Fig. 7). While organic N

represented ≤5% of discharge and NH4 accounted for <0.7% of N discharge. Since 2008, there

appears to be an increase in the percent contribution of NO3 (with corresponding decreases in

NH4 and organic N) (Fig 7). Given that the FSSD discharge is relatively constant (Fig 6A) so

that surface water N in the receiving waters of Boynton Slough should vary as a function of

freshwater input that serves to dilute the N load.

Near-field sampling of FSSD effluent discharge for total N, total ammonia, and total P

was conducted to FSSD personnel as part of National Pollution Discharge Elimination System

(NPDES) permitting. Samples were collected at two locations in Boynton Slough (at 100ft from

effluent discharge and at the intersection of Boynton and Suisun Sloughs) and at the intersection

of Peytonia and Suisun Slough (Table 4). Mean total N concentrations within

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Table 4. Near-field nutrient samples for total N, total ammonia and p=total phosphorus. Samples

were collected by the FSSD staff between February 2012 and January 2015 at three stations in

Boynton and Peytonia Slough in western Suisun Marsh. Samples were collected quarterly.

Boynton @ 100 ft

from FSSD Discharge (RSW 1)

Boynton @ Suisun Slough

(RSW 4)

Peytonia @ Suisun Slough

(RSW 6)

Total nitrogen (mg N L-1 ; n =13)

12.7

(1.8 – 34.7)

4.2

(1.5 – 17.6)

4.7

(2.1 – 18.2)

Total ammonia (mg N L-1 ; n =13)

0.25

(0.03 – 1.68)

0.14

(0.03 – 0.23)

0.13

(0.03 – 0.21)

Total phosphorus (mg P L-1; n =13)

1.81

(0.3 – 4.4)

0.42

(0.1 – 0.7)

0.55

(0.3 – 0.8)

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Boynton Slough 100 feet from the FSSD outfall were 12.7 mg N L-1;mean total ammonia

concentrations were 0.25mg N L-1, or roughly 2% of the total N. Total Phosphorus was 1.81 mg

P L-1. At the intersection of Boynton Slough and Suisun Slough, total N concentrations declined

to 4.2 mg N L-1, a decrease of approximately 66%. Total ammonia concentrations were reduced

by ~50%. Total P at the intersection of Boynton and Suisun Sloughs declined by >70% from

concentrations near the WWTP outfall. Total N and total ammonia concentrations in Peytonia

Slough (at its intersection with Suisun Slough) were comparable to the downstream station at

Boynton Slough; total P concentrations were 0.55mg P L-1, a 30% increase over the downstream

Boynton Slough station.

The potential for cultural eutrophication (excessive algal biomass) and subsequent

hypoxia can be assessed based on these near-field N concentrations, assuming that: 1)

phytoplankton can assimilate all of the available N, 2) build biomass according to the canonical

Redfield Ratio for phytoplankton of 106 C : 16 N (and build chlorophyll-a at a ratio of 1µg chl-a

L-1 : 1 µmol N L-1) , and 3) that every mol C respired requires 1 mol O2 (DO). Assuming an

average of 4 mg N L-1 (approximate N concentration of Boynton and Peytonia Sloughs as they

intersect with Suisun Slough), would result in chlorophyll-a >> 300 µg L-1, and BOD far in

excess of dissolved oxygen at saturation (BOD >> 50mg DO L-1), resulting in anoxia. In

contrast, Parker and Cohen (2011) reported chlorophyll-a concentrations in the range of 5 to 25

ug L-1 seasonally in western Suisun Marsh sloughs, including Boynton and Peytonia Sloughs.

While the scenario of complete conversion of DIN into phytoplankton biomass is highly unlikely

within Suisun Marsh sloughs (due to phytoplankton losses and advection and non-autotrophic

transformations of N, such a scenario could occur within managed wetlands. Thébault et al

(2008) estimated high rates of primary production in the open water habitats associated with the

South Bay Salt Pond Restoration Program. The system was very sensitive to small changes in the

balance in production and respiration, with periodic oxygen depletion. The impact of anoxia

within managed wetlands would depend on the amount of dilution that would occur within

sloughs as the managed wetland was drained.

Nutrient Monitoring by the San Francisco Bay National Estuarine Research Reserve The SF Bay NERR has been monitoring nutrients and related parameters since May 2008

at two monitoring stations located within the Rush Ranch Open Space Preserve (Rush Ranch),

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which includes a significant region of historic tidal marsh adjacent to the Potrero Hills in western

Suisun Marsh. The two monitoring stations are located at the intersections of Cutoff Slough with

First Mallard Slough (38° 11' 41.70 N, 122° 1' 58.02 W) and Second Mallard Slough (38° 10'

59.40 N, 122° 0' 46.68 W) (Fig. 1). Cutoff Slough is a major offshoot of Suisun Slough and

connects to Montezuma Slough, which then connects to Suisun Bay. Each of the Mallard

Sloughs innervates different regions of the tidal marsh at Rush Ranch. First Mallard Slough and

its associated creeks encompass the northwestern portion of Rush Ranch and receive seasonal

runoff from the Potrero Hills, including potential runoff extending from the area around the

Potrero Hills Landfill, the Rush Ranch nature center and headquarters area, and both private and

public grasslands primarily used for grazing cattle. As First Mallard Slough grades into the

uplands it becomes Spring Branch Creek, the lower portion of which has been modified with a

levee across the tidal end and therefore is subject to restricted tidal exchange (Olson 2012). That

lower portion of Spring Branch Creek is slated to be restored to fully tidal habitat in the near

future, a modification that will likely impact water quality along the length of First Mallard

Slough. In contrast, Second Mallard Slough and its associated creeks encompass the southeastern

areas of the marsh at Rush Ranch and receive little or no watershed input of freshwater other

than direct precipitation. Water quality measured at the SF Bay NERR monitoring station at the

mouth of Second Mallard Slough is more indicative of the conditions in the main stem of

Montezuma Slough and appears to be consistently less affected than First Mallard Slough by

land use practices in the Potrero Hills and associated uplands. It has been suggested that Second

Mallard Slough could be considered to represent a “reference site” within Suisun Marsh and for

some analyses First Mallard Slough may also be considered a regional reference site.

The SF Bay NERR water-quality monitoring stations are mounted on treated wood

pilings placed approximately 10 meters into the entrance of the sloughs and a third of the width

across the slough. At each of these stations, the SF Bay NERR maintains a data sonde positioned

within a meter above the sediment surface that records near-continuous (every 15 min)

measurements of water depth, temperature, conductivity / salinity, pH, dissolved oxygen,

turbidity and in some cases chlorophyll-a fluorescence. Additionally, once monthly at each of

these monitoring stations the SF Bay NERR measures concentrations of chlorophyll-a and

inorganic nutrients in discrete water samples collected adjacent to each data sonde. Replicate

water samples are taken within five minutes of one another and within the three hours before low

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tide using a Niskin bottle lowered to the depth of the sonde. These samples provide additional

insight into spatial and temporal differences in water quality in these two natural tidal sloughs

and represent a basis for future comparison with additional sites.

Water for all analytes except extracted chlorophyll-a is stored in a clean ISCO

polyethylene sample bottle that has been rinsed two times with ambient water. A subsample from

the Niskin bottle, for later determination of chlorophyll-a , is stored in an amber Nalgene bottle

after two rinses with ambient water. Bottles are stored on ice during transport to the laboratory at

Rush Ranch where samples are filtered and then either analyzed for concentrations of NH4 and

chlorophyll-a or frozen for subsequent analysis of the remaining analytes (NO3, NO2, PO4, and

Si(OH)4). Urea was also measured as part of the monthly water sampling at these stations for

several years during the monitoring period, and although technically not part of the DIN pool, we

will consider urea along with DIN as has become the convention with the shift to urea-based

fertilizers (e.g., Glibert et al. 2006).

General Patterns in Meteorological Conditions at Rush Ranch Open Space Preserve and Water Quality Conditions in First and Second Mallard Sloughs Air temperature at Rush Ranch varied seasonally from about 5-30 °C between 2008 and

2014 (Fig. 8A). Photosynthetically active radiation also followed seasonal expectations with

highest values occurring around the summer solstice (Fig. 8A). Wind speeds showed seasonality

with strongest winds (6 m sec-1) occurring in mid-summer and lower wind speeds (≤2 m sec-1) in

winter (Fig. 8B). Higher wind speeds observed in summer lead to mixing in the water column

and declines in water-column transparency. Rainfall (precipitation) was recorded during the late

fall through early spring (Fig. 8B). Rainfall was above average in 2011 and was followed by four

successive winters with below average precipitation for the region. The effect of inter-annual

variability in rainfall on nutrients and nutrient indicators that occurred during this data record is

explored in more detail below.

Mean daily water temperature at First and Second Mallard Sloughs ranged between 8-24

°C with expected seasonal patterns of low temperatures in winter and warming through summer

and fall (Fig 9 A, C). Salinity varied between winter lows of <2 (on the practical salinity scale) to

>8 with lower salinity occurring in spring and higher salinity in fall (Fig. 9B, D). During the

period between early 2011 through mid-summer 2012, salinity was lower than the comparable

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timeframe for other years, reflecting the above average rainfall in 2011. Turbidity increased in

early spring in 2009 (likely associated with a rainfall event) and also during each summer period,

likely associated with seasonal increases in wind speed described above.

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General Patterns in Nutrient and Chlorophyll-a Concentrations in First and Second Mallard Sloughs Monthly averages of nutrient concentrations were significantly higher in First Mallard

Slough for NO3, NH4, urea and PO4 compared with concentrations in Second Mallard Slough

(Fig. 10 and 11), but Si(OH)4 concentrations were not significantly different between the sloughs

(Fig. 11 B, Table 5). The differences in DIN and P concentrations observed between these

adjacent sloughs indicate either differences in hydrologic connectivity with other sloughs in the

marsh, or an indication of the marked differences in watershed loadings. The nutrient modeling

provided by Tetra Tech (see “Nutrient Discharge from the Fairfield Suisun Sanitation District

Outfall in Boynton Slough” section) suggest the potential that elevated nutrients at First Mallard

Slough could have originated at FSSD. The similarity in Si(OH)4 with Second Mallard Slough is

also supportive of this idea as it does not have a significant anthropogenic signal (i.e., from either

WWTP effluent or anthropogenic watershed sources).

Total DIN concentrations were consistently different between First and Second Mallard

Sloughs, although the percent contribution of each of the major forms of DIN (i.e., NO3 and

NH4) was similar in each slough (Table 6). Notably, the ratio of DIN to PO4 was 8.08 and 10.4

(mol : mol) in First and Second Mallard Sloughs, respectively. This would imply, based solely

on phytoplankton nutrient drawdown and an assumed Redfield Ratio (i.e., N:P ratio of 16), that

in these sloughs DIN would limit phytoplankton growth before PO4, consistent with the analysis

of Tetra Tech (2013) for western Suisun Marsh sloughs. Silicate was also found in relative

abundance in both sloughs. Using the same logic as above, and assuming a N:Si ratio of 1 for

diatoms (Brzezinski 1985), as diatoms assimilate N and Si for biomass production N would limit

diatom growth well before any potential for Si limitation. Taken together, these results suggest

that presently under conditions when phytoplankton could completely utilize available nutrients

(e.g., in areas with long water residence time), nitrogen availability would limit primary

production, and PO4 and Si(OH)4 concentrations would go unutilized.

Average chlorophyll-a concentrations in First Mallard Slough were higher than in Second

Mallard Slough, although these differences were not significant (Fig. 11C, Table 5) and both

sloughs showed some seasonality with respect to elevated chlorophyll-a concentrations, (i.e.,

higher concentrations observed during Spring and Fall Figure 11C). Within these two sloughs,

chlorophyll-a concentrations were generally < 10 µg L-1 (79% and 84% of all measurements

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Table 5: Mean (and range) concentrations of inorganic nutrients at First and Second Mallard

Sloughs. Dataset are from monthly grab samples in both sloughs between May 2008 and January

2015 for NO3, NH4, PO4 and Si(OH4). Urea concentrations were determined between May

2008 and June 2013.

First Mallard Slough Second Mallard Slough Difference

Nutrient

n

Conc.

Mean

(min – Max)

N

Conc.

Mean

(min – Max)

Signif. (P

value)

Students t -

test

NO3 (mg N L-1) 82 0.96

(0.06 – 2.41) 81

0.42

(0.00 – 1.11) <0.001

NH4 (mg N L-1) 55 0.13

(0.01 – 0.49) 74

0.06

(0.00 – 0.20) <0.001

Urea (mg N L-1) 63 0.04

(0.00 – 0.21) 63

0.03

(0.00 – 0.18) <0.001

PO4 (mg P L-1) 82 0.31

(0.05 – 2.45) 81

0.11

(0.05 – 0.84) <0.001

Si (mg Si L-1) 82 5.43

(0.11 – 9.51) 81

5.68

(0.03 – 10.24) 0.47

Chlorophyll a

(µg L-1) 72

7.9

(0.5 – 52.8) 73

6.2

(0.9 – 37.7) 0.19

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Table 6: Fraction of nitrogen form for total dissolved inorganic nitrogen at First and Second

Mallard Sloughs. Nitrogen to Phosphorus to silicate ratio (mol :mol) for comparison with the

canonical Redfield Ratio for phytoplankton (modified by Brzezinski (1985) for diatoms) = 16N :

1 P : 16 Si.

First Mallard Slough Second Mallard Slough

Conc (µmol L-

1)

% of

DIN Conc (µmol L-1)

% of

DIN

NO3 68.6 85 30.0 82

NH4 9.3 12 4.3 12

Urea 2.9 4 2.1 6

∑DIN 80.8 100 36.4 100

PO4 10.0 --- 3.5 ---

Si(OH)4 194 --- 203 ---

N : P : Si 8.08 : 1 : 19.4 --- 10.4 : 1 : 58 ---

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made in First and Second Mallard Sloughs, respectively); approximately 15% of samples had

chlorophyll-a concentrations between 10 – 30 µg L-1 in both sloughs, whereas 6% and 1% of

chlorophyll-a concentrations were in excess of 30 µg L-1 in First and Second Mallard Sloughs,

respectively (Fig 12). Although the highest chlorophyll-a concentrations were more commonly

found in First Mallard Slough (consistent with the significantly elevated nutrients also observed

there), it is not clear that elevated nutrients represent the driver of high biomass in the sloughs;

the elevated chlorophyll-a found in the sloughs may be more a function of tidal flushing rates in

both sloughs and their associated creek networks, impact of duck club management (with

discharge of water from managed wetlands also occurring during spring and fall) or tidal

overtopping of the marsh plain. These drivers should be investigated as a potential mechanism

supporting higher chlorophyll-a concentrations.

Given that chlorophyll-a of 30 to 50 µg L-1 occur at First and Second Mallard Sloughs

only infrequently (Fig. 12), these concentrations represent a “worst case” scenario of cultural

eutrophication for these sloughs and previous reports and personal observations have suggested

that Suisun Marsh sloughs can support large phytoplankton blooms (Muller-Solger and

Bergamaschi 2005) that are a potential source of BOD. A simple calculation of the BOD that

would result from the remineralization of this amount of phytoplankton biomass can be made

based on the assumption that the average phytoplankton cell contains 35 µg C : 1 µg chlorophyll-

a and that every mol C respired required 1 mol O2 (DO); thus, the biochemical oxygen demand

associated with 50 µg L-1 chlorophyll-a is equivalent to 4.7 mg DO L-1 BOD.

Clearly this amount of BOD should raise concerns, however at least some fraction (and

potentially a large fraction) of the chlorophyll-a contained in pelagic phytoplankton is likely

consumed by higher trophic levels within the marsh and/or moved outside of the marsh through

tidal advection or trophic relay. Elevated chlorophyll-a events in these sloughs were not

associated with sags in DO (see discussion below).

Seasonal Differences in Nutrient and Chlorophyll-a Concentrations in First and Second Mallard Sloughs In order to investigate seasonal trends in nutrients and chlorophyll-a concentrations in

First and Second Mallard Sloughs, we followed the approach of Wilkerson et al. (2006) and

calculated seasonal mean concentrations with spring defined as all sampling that occurred

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between March 1 and May 31, summer between June 1 and August 31, fall between September 1

and November 30, and winter between December 1 and the end of February.

Consistent seasonal patterns were observed in First and Second Mallard Sloughs for each

of the nutrients measured. Nitrate concentrations were typically highest during the spring and

declined through summer and fall before increasing again in winter; fall NO3 concentrations

were more variable than in other seasons (Fig 13A,D). Nitrite concentrations were nearly two

orders of magnitude lower than NO3 and were typically highest in spring and fall (Fig. 13B,E),

with lower values observed in summer and winter. Nitrite is not usually associated with nutrient

impairment but elevated NO2 concentrations are often used as a proxy of nitrification, with the

buildup of NO2 representing a decoupling of the two step nitrification process (NH4 NO2 and

NO2 NO3). The increase of nitrite in spring and fall is consistent with nitrification occurring in

managed wetlands with a build-up of NO2. Nitrite may then be subsequently discharged into

Suisun Marsh sloughs; elevated nitrite in fall is also consistent with the potential for a

temperature driven increase in nitrification rates.

Ammonium concentrations were approximately one order of magnitude lower than

nitrate concentrations (Fig. 13 C, F). Relatively low NH4 was observed in spring, with further

declines in summer. The slightly elevated NH4 concentrations observed during spring may be

due to discharge of remineralzed NH4 from managed wetlands or from sediment release within

the slough habitats themselves. During the fall period, NH4 concentrations increased markedly,

especially in First Mallard Slough (Fig. 13 C). This seasonal elevation in NH4 concentrations

may reflect NH4 remineralization occurring after the summer build-up of algal biomass and

terrestrial organic matter in managed wetlands that is discharged into surrounding sloughs during

the draining cycles. Alternatively, the elevated NH4 load may be due to early-season storm water

runoff from grazing lands in the Potrero Hills. Under either scenario, increased NH4

concentrations are likely exacerbated by elevated air and water temperatures experienced in

Suisun Marsh in fall which may increase remineralization rates. Winter NH4 concentrations were

similar between the sloughs and less variable than during the fall in First Mallard Slough and

slightly elevated compared to fall in Second Mallard Slough (Fig. 13C,F).

Patterns in urea concentrations were similar to those observed for NO3, with peak

concentrations in spring, possibly due to seasonal runoff, followed by declines in summer and

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fall and subsequent increase during winter (Fig 14C, F). The apparent high variability in urea

concentrations may be a function of relatively low concentrations overall relative to analytical

precision in the laboratory methods of analysis. Phosphate concentrations also showed relatively

high variability within seasons, especially during spring and winter, but mean concentrations of

PO4 were similar across seasons in both First and Second Mallard Sloughs (Fig. 14 A,D). Silicate

concentrations were high (≥6 mg Si L-1) during all seasons and showed consistent peaks in

spring and summer with a decline during fall (in both First and Second Mallard Sloughs) and

winter (in First Mallard Slough) (Fig. 14 B,E). Elevated Si(OH)4 in spring may be a reflection of

seasonal precipitation that delivers Si(OH)4 to the SFE from the Sierra Mountains.

Seasonal peaks in chlorophyll-a concentrations and phaeophytin (a degradation product

of chlorophyll-a) were observed in spring and fall with large variability during these seasons,

possibly reflecting the ephemeral nature of chlorophyll-a in Suisun Marsh (Fig. 15). During

summer, mean chlorophyll-a concentrations were similar to both spring and fall averages but

were generally less variable. Winter chlorophyll-a concentrations were lower than for other

seasons.

Inter-annual Trends in Nutrient and Chlorophyll-a Concentrations in First and Second Mallard Sloughs Inter-annual trends in nutrient and chlorophyll-a concentrations were explored for each

season during 2008 to 2014 (Figs. 16 and 17). Within First Mallard Slough, average NO3

concentrations appeared to have increased from 2008-2012 before declining during 2013-2014.

This pattern held in all seasons except spring 2014, when elevated NO3 was observed in First

Mallard Slough (Fig. 16A). These inter-annual patterns are not as clear for Second Mallard

Slough, suggesting that the patterns observed in First Mallard Slough may be the result of

changes in land management practices or wetland activities that are local to that slough. Unlike

the patterns observed for NO3, inter-annual trends in NH4 concentrations varied by season (Fig.

16C). Ammonium concentrations were highest (0.3 to 0.4 mg N L-1) during fall of 2008-2010

and then declined to <2 mg N L-1 from 2011-2014. Concentrations of NH4in spring were

relatively constant and low (<0.1mg N L-1) throughout the data record, except for 2010 which, on

average, experienced twice the typical concentrations of NH4. Similarly, NH4 concentrations

were consistently low (<<0.1mg N L-1) for the majority of the data record (note: there are no

mean summer data on NH4 concentrations for 2009 and 2010), except for substantially elevated

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NH4 in First Mallard Slough observed during summer 2008. Finally, average winter

concentrations of NH4 increased from 2008-2010 before declining between 2011-2014 (note:

there is no average concentration of NH4 reported for winter 2012).

No clear inter-annual trends appear in PO4 concentrations between 2008 and 2014 (Fig

17A). There are some indications of annual increases in PO4 especially for fall and summer.

Apparent in this analysis is elevated PO4 during winter 2009 and into spring 2010 in First

Mallard Slough, although the reason for the increase is not clear. Inter-annual patterns in Si(OH)4

concentrations suggest lower concentrations in 2008 and 2009 relative to later in the data set, this

is especially true during fall and winter (Fig. 17B). These patterns may reflect below average

rainfall in these years that led to diminished supply of Si(OH)4 to the SFE, although 2013 and

2014 were similarly dry and are characterized as relatively high Si(OH)4 conditions.

Average fall chlorophyll-a concentrations were relatively low between 2008 and 2011,

but increased nearly two-fold during 2012 and 2013, suggesting a shift towards larger fall

phytoplankton blooms, but during 2014, average fall chlorophyll-a concentrations were again

low (Fig. 18). Average spring chlorophyll-a concentrations were elevated between 2009 and

2011 and then declined between 2012 and 2014, suggesting a reduction in the spring

phytoplankton bloom in First Mallard Slough. Average summer chlorophyll-a concentrations

appeared to decline from 2008 to 2011 before increasing somewhat in 2012 and showing large

increases during 2013 and 2014. These inter-annual trends in chlorophyll-a concentrations

present a picture of diminished phytoplankton growth during spring, and an increase in the

prevalence of summer and fall accumulations of phytoplankton biomass (Fig. 18). Although

speculative, this may be associated with changes in phytoplankton community structure, for

example through a prevalence of taxa that would be favored in the warmer water found in Suisun

Marsh during the summer – autumn period. Average winter chlorophyll-a concentrations were

consistently low with some indication of lower chlorophyll-a concentrations in later years 2013-

2014.

The Influence of Rain Events on Nutrient Concentrations in First and Second Mallard Sloughs The influence of precipitation on nutrient and chlorophyll-a concentrations in First

Mallard Slough were examined by summing rainfall totals that occurred in A) three days, B) one

week and C) two weeks prior to measured nutrient and chlorophyll-a concentrations (Figs. 19

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and 20). Immediately following precipitation events (i.e., three-day cumulative rainfall) there

appeared to be a relationship between the amount of precipitation and concentrations of either

NO3, NH4 or chlorophyll-a (Figs. 19 A,D, 20A) with precipitation increases reducing both NO3

and chlorophyll-a (Fig. 19A,D). That pattern still holds but is less clear when the precipitation

window is extended to one week of cumulative rainfall (Fig 19 B,E). The effects of two weeks of

cumulative precipitation are still apparent as diminished chlorophyll-a concentrations but not

diminished NO3 concentrations (Fig. 19 C,F). Instances when elevated chlorophyll-a and NO3

concentrations are preceded by periods of little or no precipitation suggest that rainfall and the

subsequent runoff from the watershed do not always substantially augment NO3 concentrations,

but may rather serve to dilute NO3-rich water originating from another source. Increased

precipitation events that lead to decreases in chlorophyll-a concentrations likely reflect a similar

dilution response via advection of chlorophyll-a out of sloughs or a decrease in water column

transparency. These same patterns are also observed for NH4 concentrations (Fig. 20).

The Relationship between Dissolved Oxygen, Chlorophyll-a and Nutrient Concentrations in First and Second Mallard Sloughs The relationships between DO (a proposed nutrient impairment indicator) and the

concentrations of nutrients, and pelagic chlorophyll-a (another proposed indicator) were

investigated using the SF Bay NERR dataset (Fig. 21). Pooled data from both First and Second

Mallard Sloughs revealed no discernable relationship between NO3 or PO4 concentrations DO

concentration (mg DO L-1) or DO percent saturation (percent saturation, corrects for

temperature-dependence of DO concentrations but not atmospheric exchange). Dissolved oxygen

percent saturation varied across a range of <40% to ≈100% of saturation in the SF Bay NERR

dataset. There does appear to be a positive relationship between chlorophyll-a concentrations and

DO percent saturation of dissolved oxygen at chlorophyll-a concentrations greater than 20 µg L-1

(Fig. 21A). As concentrations of chlorophyll-a increase above 30 µg L-1, DO is generally close

to saturation. This relationship is most likely the result of the relatively high rates of primary

production by algal populations within these sloughs which allows them to keep up with BOD

(Fig. 21A).

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Broad Spatial Sampling of Nutrient Concentrations and Related Water Quality Parameters in Suisun Marsh from 2007-2008 Between June 2007 and May 2008, up to seven locations broadly distributed across

Suisun Marsh were sampled as part of a CALFED-sponsored study. Although this data set

provides better spatial coverage than the SF Bay NERR dataset that is constrained to two

sloughs, it lacks temporal resolution beyond a single year. Results of this study were summarized

by Parker and Cohen (2010) in the SF Bay NERR Site Profile (Ferner 2011). Here we reinterpret

these data in the context of the SF Bay NERR monitoring data presented above. Detailed

methods for sample collection are provided in Parker and Cohen (2010) and briefly summarized

below.

Seven open water tidal slough habitats (Fig. 1) were visited monthly; three of these

sloughs (Boynton, Peytonia and Sheldrake sloughs) are located in western Suisun Marsh and

were characterized with respect to nutrients by Tetra Tech (2013). As previously noted, both

Boynton and Peytonia sloughs experience low dissolved oxygen events during late spring and in

fall (Siegel et al. 2011) and Boynton Slough is the receiving water for wastewater discharge from

the Fairfield Suisun Sanitation District (described above). Three additional open water habitats

were sampled in the eastern Suisun Marsh, including Little Honker Bay, Denverton slough and

Nurse Sloughs. Montezuma Slough was sampled to provide a central marsh location. Nutrient

concentrations were compared with the open water central channel of Suisun Bay (US

Geological Survey station 6; 38° 03.9” N, 122° 02.1”W; http://sfbay.wr.usgs.gov/access/wqdata/

overview/wherewhen/where.html) as a reference to contrast patterns within Suisun Marsh to the

northern SFE. Nutrient concentrations in Suisun Marsh were generally higher than

concentrations found in adjacent Suisun Bay.

Nutrient concentrations in Suisun Marsh were higher in the western sloughs compared to

eastern sloughs, presumably a result of wastewater nutrient loading from the FSSD outfall to

Boynton Slough (Figure 22). NO3 averaged >100 µmol L-1 (> 1.4 mg L-1) for all but fall; these

concentrations are roughly 40% higher than the average NO3 values measured by the SF Bay

NERR in First Mallard Slough and three-fold higher than average values in Second Mallard

Slough (Fig. 22A). These NO3 concentrations are lower than those reported for Boynton Slough

by Tetra Tech (2013), likely reflecting the distance of the sampling station from the FSSD

outfall. Nitrate concentrations in eastern Suisun Marsh were 20% to 25% of the values reported

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in Western Suisun Marsh during all seasons. NH4 concentrations ranged between 0.62 and 4.70

µmol L-1 (0.08 and 0.56 mg N L-1) across all sloughs except during winter when NH4 was > 15

µmol L-1 (0.60 mg N L-1) (Fig. 22D). These NH4 concentrations are roughly comparable to those

reported by Tetra Tech (2013) and measured by SF Bay NERR at First and Second Mallard

Sloughs for all but winter, where NH4 concentrations at the SF Bay NERR sites were ≤ 0 .20 mg

N L-1 during the winter. Interestingly, early within the SF Bay NERR record (2008 – 2010) NH4

concentrations during fall in First Mallard Slough were substantially higher (≥0.4 mg N L-1) and

more similar to the results obtained in 2007 and 2008 by Parker and Cohen (2010). Parker and

Cohen (2010) suggested that high NH4 during the winter may have been due to reduced demand

by vascular salt marsh plants; alternatively, the elevated NH4 may in fact be reflective of

operations of managed wetlands and the discharge of regenerated NH4 within the duck clubs.

Like NO3, PO4 was also elevated in the western sloughs, ranging between 6.7 and 15.6 µmol L-1

(0.21 – 0.48 mg P L-1) (Fig. 22C), quite consistent with mean SF Bay NERR values of 0.31 mg P

L-1 but lower than reported by Tetra Tech (2013). Phosphate concentrations in the central and

eastern sloughs in spring, summer and fall were between 0.38 – 4.7 µmol L-1 (0.01 0.15 mg P L-

1) or at most 50% of SF Bay NERR values, and at or below method detection limits (0.05 µmol

L-1 or 0.002 mg P L-1) during winter. Silicate concentrations were always >100 µmol L-1 (2.8

mg Si L-1) across sloughs but were lower than the grand average for the SF Bay NERR data set

in First and Second Mallard Sloughs (5.43 mg Si L-1) or the seasonal average for Si(OH)4 in

adjacent Suisun Bay (Wilkerson, et al., 2006).

Chlorophyll-a concentrations in Suisun Marsh were always higher than average

chlorophyll-a previously reported for USGS Station 6 in Suisun Bay (Wilkerson et al., 2006)

(Fig. 22E). Overall, differences in chlorophyll-a between locations within the marsh were greater

than seasonal differences. During winter and spring, chlorophyll-a concentrations were similar in

all sloughs, with spring chlorophyll-a concentrations 60% higher than winter values. During the

summer and fall, chlorophyll-a concentrations in the eastern sloughs increased slightly above

spring values and were nearly 3-fold higher than western sloughs. Mean chlorophyll-a

concentrations in western sloughs varied between summer lows of 6.0 µg L-1 to highest values in

winter 13.8 µg L-1). The average winter chlorophyll-a encompassed large variability with one

sample collection of nearly 46 µg L-1; removing this one observation results in mean winter

chlorophyll- a of 8.7 µg L-1. This is more consistent with average winter chlorophyll-a measured

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by the SF Bay NERR at First and Second Mallard Sloughs. Elevated chlorophyll-a values

observed in the eastern slough may be a function of longer water residence times compared to

the western sloughs which are adjacent to Suisun slough, the major conduit to Grizzly Bay and

the SFE.

Nutrient Data from the Moyle Laboratory, UC Davis Additional nutrient data are available from surface water samples collected at a variety of

locations around Suisun Marsh during monthly fish trawling trips by Peter Moyle’s laboratory at

the University of California, Davis (Fig. 23). During each monthly trip, samples were brought on

board, filtered and kept on ice for analysis and reporting (in mg N L-1). Elevated nutrient

concentrations in First Mallard Slough (referred to in the figure as Spring Branch, SB) are likely

the result of some combination of (1) water exchange with Suisun and Boynton Sloughs that

includes FSSD WTTP discharge, (2) runoff from the Potrero Hills that includes nutrients derived

from cattle grazing and grassland management, and (3) non-point pollution and surface runoff

from the large urban areas of Fairfield and Suisun City, agricultural lands in the foothills, and

cattle grazing areas near the FSSD WTTP. Additional data from a special study in First Mallard

Slough during May-June 2014 provide some suggestion that initial overtopping of the marsh

plain introduces nutrients into subtidal sloughs during seasonally high spring tides (Fig. 24).

Initial Conclusions and Recommendations

The goal of this report was to: 1) provide a context for understanding the potential for

nutrient impairment of tidal wetlands, specifically Suisun Marsh, which is currently listed as

impaired by nutrients, 2) develop conceptual models and response indicators that could be used

to assess the potential for nutrient impairment using the numeric nutrient endpoint (NNE)

framework as a guide, and 3) synthesize existing data for Suisun Marsh with respect to nutrient

and impairment indicators. Although tidal wetlands are generally regarded as ecosystems that

serve to buffer the influence of anthropogenic nutrient loads (e.g., from watersheds and point

sources like WWTP discharge) on coastal waters and estuaries, there is little doubt that

anthropogenic nutrients supplied to tidal wetlands have the potential to impair ecosystem health.

The simple conceptual models provided here suggest that pelagic chlorophyll-a and dissolved

oxygen concentrations may be good candidates for assessing such nutrient impacts via cultural

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eutrophication pathways leading to hypoxia events. However, limiting nutrient impact

assessment solely to analysis of chlorophyll-a and dissolved oxygen is likely insufficient for

capturing a range of potential impacts.

Unfortunately, as noted previously (e.g., Tetra Tech 2013) water quality and nutrient data

within Suisun Marsh is limited both spatially and temporally and additional indicators of nutrient

impairment have not previously been considered. Thus data for other potential indicators such as

microphytobenthos or emergent vegetation metrics do not exist. The NNE effort currently

underway for the SFE considers phytoplankton species compositional shifts, including the

concentrations of harmful algal bloom cells and their associated toxins, as indicators of nutrient

impairment. Again, a lack of baseline data for these indicators in Suisun Marsh makes their

utility limited. As a result, the third aim of this report, synthesizing of existing nutrient and

indicator data, is also limited with respect to our overall conclusions about nutrient impairment.

Lack of Evidence for Nutrient impairment of Ecosystem Health in Suisun Marsh

Considering the spatially constrained monitoring data that are available, nutrient loading

in Suisun Marsh does not appear to be the major driver of impaired ecosystem health via

excessive phytoplankton growth or declines in dissolved oxygen. These conclusions are based on

analysis for western Suisun Marsh and are the sites that have previously shown indication of

ecosystem health impairments (i.e., low dissolved oxygen). The limited investigation into

eastern Suisun Marsh suggests that neither chlorophyll-a or nutrient concentrations are found at

concentrations that are outside of the range reported for the western marsh sites.

Pelagic chlorophyll-a concentrations are elevated within slough habitats of Suisun Marsh

relative to Suisun Bay. This is not particularly surprising given longer water residence times

within the marsh and is supported by the single year of spatial sampling within sloughs of

western and eastern Suisun Marsh (Parker and Cohen 2011). Interestingly, the western sloughs,

where nutrient concentrations are highest, do not always support the highest chlorophyll-a

concentrations in Suisun Marsh. Based on the seven year time series of nutrient and chlorophyll-

a concentrations in western slough habitats (First and Second Mallard Sloughs) there are

relatively rare occurrences (≤5% of all observations) when chlorophyll-a concentrations are

substantially elevated over average conditions.

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Initial Recommendations for Monitoring of Indicators of Potential Nutrient Impairment in Suisun Marsh

Increase Temporal and Spatial Coverage of Nutrient Monitoring in Suisun Marsh

Significant data gaps exist for the assessment of the potential for nutrient impairment in

Suisun Marsh. Paramount among these is the limited spatial coverage of routine monitoring of

nutrient concentrations (Siegel et al. 2011; Tetra Tech 2013). Ongoing monitoring by SF Bay

NERR will provide data on nutrient, pelagic chlorophyll-a, and dissolved oxygen concentrations,

as well as ancillary data collection within First and Second Mallard Sloughs. This federally

funded monitoring program could serve as a useful model for further development of a

coordinated water-quality monitoring program throughout Suisun Marsh.

Given the importance of tidal processes in the transport of nutrients and organic matter,

the frequency of nutrient sampling should be increased from the monthly grab samples that are

currently being collected. Investigation into the exchange of water and nutrients between habitats

in Suisun Marsh represents a high priority area for future research. Sampling that encompasses

spring – neap cycles will be necessary to fully understand nutrient dynamics and responses of

impairment indicators. During monthly spring tides, there will be increased connectivity between

the upper intertidal habitats and the subtidal sloughs due to overtopping and draining of the

marsh plain and those connections should be greatest during winter and summer spring tides.

At least one additional regular nutrient monitoring platform should be established in

Suisun Marsh that allows for monitoring of conditions in eastern Suisun Marsh (the Denverton –

Nurse Sloughs and Little Honker Bay). This region of the Marsh likely has longer water

residence time, includes shallow open water habitat (i.e., Little Honker Bay) and includes both

managed wetlands (e.g., Luco Pond) and restored tidal wetlands (e.g., Blacklock Tidal Marsh).

We are aware that special studies are occurring in these habitats (e.g., John Durand, UC Davis,

and Shannon Strong, SFSU) and we would encourage synthesis of these project findings once

those studies have concluded and the data are made available.

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Establish Sampling of Microphytobenthic Chlorophyll-a and SAV / Macroalgae Cover at

Several Fixed Geography Stations

There is no existing monitoring of benthic chlorophyll-a in Suisun Marsh and relatively

little information regarding microphytobenthos for the SFE generally. A monitoring program that

includes regular sampling for benthic chlorophyll-a could be implemented and sited as part of

the pelagic nutrients and chlorophyll-a monitoring program referred to above.

Given the amount of recreational and scientific study that is occurring in the sloughs of

Suisun Marsh, it is unlikely that widespread problems with SAV and macroalgae are occurring

and not being reported. Still, with changes in SAV in the Delta and identification of SAV in

Suisun Marsh some effort to conduct regular (quarterly) spatial assessments of SAV and

macroalgal cover in Suisun Marsh may provide a useful metric of nutrient impairment. A

conceptual model for SAV / macroalgae is provided as an appendix at the end of this report.

Establish Collaborative Nutrient –Impairment Indicator Monitoring at Selected Managed

Wetlands

Because much of the documented impairments to ecosystem health (i.e., periodic hypoxic

events) are associated with activities within managed wetland habitats in Suisun Marsh (Siegel et

al. 2011), we strongly advise to work collaboratively with managers of these habitats across

Suisun Marsh to evaluate the influence of specific management actions on nutrients and nutrient-

related processes. In addition to serving as sources of organic matter through soil leachate

(Siegel et al. 2011), there is reasonable potential that managed wetland habitats serve as

phytoplankton “incubators” during periods of water retention (primarily during fall and

intermittently during spring).

Collaborative work with managers of these habitats should be initiated to regularly

monitor nutrient concentrations and indicators (especially pelagic phytoplankton). Some of this

work may be occurring already but incorporating these sampling schemes into a single

monitoring program would help to elucidate the potential nutrient – impairment linkages.

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Establish a Central Repository Suisun Marsh Nutrient and Water Quality Data

Despite the large number of scientific and monitoring activity currently underway within

Suisun Marsh, coordination of data sharing for synthesis and resource management is lacking.

Acquiring nutrient and impairment indicator data sets for this report was difficult as there is no

single repository of studies or the data that result. Such a repository should be publically

available and provide information at least at the level of the types of data gathered, the agency or

entity that completed data collection, the locations and years of collection.

Promote Special Studies to Evaluate Other Potential Nutrient Impairment Indicators (i.e.,

Algal Toxins, Phytoplankton Community Composition and Alteration of Emergent Plant

Vegetation)

Both algal community composition and the occurrence of algal toxins may be valuable

nutrient impairment indicators for future assessments of nutrient impairment in Suisun Marsh.

Special studies should be supported that provide at least limited screening for harmful algal

species (e.g., Microcystis spp.) and associated algal toxins within Suisun Marsh. Additional

studies that investigate linkages between nutrient enrichment and changes in emergent

vegetation, such as the ratio of belowground to aboveground biomass in emergent vegetation, or

plant community shifts and the promotion of invasive plant species should also be undertaken.

Such studies address issues of biodiversity within the marsh and could target plant species that

are important for threatened and endangered species or those endemic to Suisun Marsh

Take Advantage of New Management Activities Planned for Suisun Marsh to Learn About

Potential Nutrient Impairments / Improvements.

Changes in the management of Suisun Marsh, such as tidal marsh restoration, alteration

of managed wetland activities, or changes in NPDES permitting represent important

opportunities to advance understanding of nutrient impairment in tidal wetlands generally, and

Suisun Marsh specifically. Capitalize on these opportunities by developing nutrient monitoring

programs that will inform management decisions. For example the lower portion of Spring

Branch Creek is slated to be restored to fully tidal habitat in the near future, a modification that

will likely impact water quality along the length of First Mallard Slough. Imminent restoration of

Hill Slough and the Goat Island Marsh (at Rush Ranch Open Space Preserve) also provide

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opportunities for productive study. Development of a nutrient monitoring program in advance of

restoration is critical in order to evaluate the impact on nutrient – marsh interactions.

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Personal Communication: Barbara Baginska – Engineering Geologist San Francisco Bay Regional Water Quality Control Board 1515 Clay Street, Suite 1400 Oakland, CA 94612 510-622-2474 bbaginska@waterboards.ca.gov

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Appendix I: Additional Indicators of Nutrient Impairment and Conceptual Models for

Suisun Marsh

Benthic Chlorophyll-a Concentrations

Similar to pelagic chlorophyll-a, sediment-associated (benthic) chlorophyll-a

concentrations are a proxy for benthic phytoplankton (microphytobenthos) biomass. Similar to

pelagic chlorophyll-a, excessive benthic chlorophyll-a may be associated with nuisance odor or

reduced aesthetics and impact beneficial uses in this regard. Also, excess microphytobenthic

production can increase organic matter cycling in the sediments and increase biochemical

oxygen demand. As described in the introduction, microphytobenthos have been used as an

index for water quality in other systems. In Suisun Marsh, this indicator of nutrient impairment is

likely restricted to intertidal areas such as the marsh surface and slough banks or where there is

sufficient light available for algal growth at the sediment surface, and the severity of impairment

is likely a function of the level and spatial extent of biomass accumulation. Still, the dynamics of

microphytobenthos are poorly understood in the SFE and may be particularly important to

ecosystem function (including impairment) in Suisun Marsh due to the large amount of intertidal

habitat in the region. The conceptual model for benthic chlorophyll-a was provided with the

model for pelagic chlorophyll-a.

Submerged and Floating Aquatic Vegetation / Macroalgae

Submerged and floating Aquatic Vegetation rooted and floating vascular plants that grow

up to the water surface but not above. Macroalgae are nonvascular primary producers that may or

may not be attached to the sediment surface. Both SAV and macroalgae can provide ecosystem

services such as refuge for fish and invertebrate species, food resources, including for waterfowl,

trapping of suspended sediments which can increase water clarity, stabilizing of sediments via

root systems, and interactions with biogeochemical cycles by increasing dissolved oxygen

concentrations (via photosynthesis) and assimilating nutrients, including nitrogen and

phosphorus. However, throughout the Delta, introductions of non-native SAV and macroalgae

have resulted in declines in ecosystem function and beneficial uses (e.g., Egeria densa, water

hyacinth; Toft et al. 2003). The amount (cover) and species of non-native SAV present in a

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system commonly provide an indicator of nutrient impairment in other systems (Maryland

Report 2001).

Conceptual Model of Nutrients and Submerged / Floating Aquatic Vegetation and

Macroalgae

A conceptual model for submerged aquatic vegetation and macroalgae is presented in

Figure 25. Submerged and floating aquatic vegetation and macroalgae require both solar

irradiance and nutrients to sustain growth. Loss of SAV and macroalgae is through grazing

(trophic transfer) or advection. If pelagic microalgal blooms reach sufficient density, they may

contribute to declines in water clarity with potentially negative consequences for submerged

aquatic vegetation, pelagic phytoplankton and the microphytobenthos. Intertidal areas where

microphytobenthos can be abundant are unlikely to be adversely affected by such changes in

water clarity. Furthermore, concentrations of suspended sediment in Suisun Marsh are already

higher than in nearby embayments like Little Honker Bay, where a thriving bed of SAV was

recently discovered (Baye and Boyer, pers. comm.), so it seems unlikely that pelagic microalgal

blooms would dramatically decrease light availability for SAV and macroalgae living in subtidal

stretches of sloughs in Suisun Marsh. A more complete understanding of these interactions

should be possible with additional information on the distribution of SAV and macroalgae as

well as routine monitoring of water clarity and the occurrence of pelagic microalgal blooms.

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