Grays Harbor Juvenile Fish Use Assessment, Literature Review

Grays Harbor Juvenile Fish Use Assessment, RCO #10-1412P

Literature Review, Habitat Inventory, and Study Plan

Prepared for the Chehalis Basin Habitat Work Group and the Salmon

Recovery Funding Board Technical Review Panel

Prepared by: Todd Sandell, Andrew McAninch and Micah Wait

Wild Fish Conservancy

January, 2011

www.wildfishconservancy.org

P.O. Box 402 Duvall, WA 98019

425-788-1167

http://www.wildfishconservancy.org/

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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Table of Contents

Project Overview ........................................................................................................ 4

Literature Review ....................................................................................................... 6

The Role of Estuaries in the Life History of Juvenile Salmon: ................................................6

Temporal Estuarine Habitat Usage: .....................................................................................8

Table 1: Temporal Habitat Use Patterns of Juvenile Pacific salmon in the Columbia Estuary: .............. 9

Spatial Estuarine Habitat Usage: ....................................................................................... 10

Study Area Overview: ............................................................................................... 11

Salmonid Species Distributions and Estuarine Use - Chehalis River Estuary: ....................... 13

1) Chinook salmon: .......................................................................................................................... 13

2) Coho salmon: .............................................................................................................................. 14

3) Chum salmon: ............................................................................................................................. 17

4) Steelhead trout: .......................................................................................................................... 17

5) Cutthroat Trout: .......................................................................................................................... 18

6) Bull Trout/Dolly Varden: ............................................................................................................. 18

Non-Salmonid/Baitfish Distributions and Estuarine Use: ................................................... 20

Habitat Inventory ..................................................................................................... 22

Figure 1: Habitat Types and Proposed Grays Harbor Estuary Sampling Sites ...................................... 24

Table 2: Summary of Grays Harbor intertidal habitat types by zone (in acres): .................................. 25

Table 3: Grays Harbor intertidal habitat types by estuary zone – ....................................................... 25

Open water and mud flats removed (in acres): ................................................................................... 25

Table 4: Proposed sampling sites (primary sites are in bold font), by zone:……………………………………..26

Table 5: Sampling site habitats, by percentage (open water and mud flats excluded): ...................... 27

Table 6: Primary site habitats, by percentage (open water and mud flats excluded): ........................ 27

Study Plan ................................................................................................................ 28

Study Objective: ............................................................................................................... 28

Study Goals: ..................................................................................................................... 28

Specific Hypotheses: ......................................................................................................... 29

2011 Sampling Plan: ......................................................................................................... 29

Sampling Permits ............................................................................................................. 32

References................................................................................................................ 33


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Project Overview

Pacific salmon that spawn in the rivers and streams of WRIA 22 and 23 all must

pass through the nearshore habitats in the Grays Harbor estuary as they migrate to the

ocean. Estuarine environments are extremely productive, rich habitats, and many life

histories of juvenile salmon spend extended periods of time rearing in this environment.

Understanding the spatial distribution, timing, species composition and relative

abundance of fish usage in these habitats is a critical component in the development of

a salmon restoration strategy for the Chehalis River basin.

The objective of this project is to develop a scientific basis for the evaluation of

potential sites for future habitat restoration and protection projects. The goals of this

project are to document the distribution, abundance, habitat use, and timing of juvenile

salmonids and other fishes in the Grays Harbor estuary, from riverine tidal waters

through marine habitats.

The first year of the Grays Harbor estuary juvenile fish use assessment project will

begin in March 2011 and continue through September 2011. The project is focused on

juvenile chinook (Oncorhynchus tshawytscha), chum (O. keta) and coho (O. kisutch)

salmon; incidental capture of steelhead trout (O. mykiss), cutthroat trout (O. clarki) and

bull trout (Salvelinus confluentus) may also occur. We will also document any

occurrence of Atlantic salmon smolts (Salmo salar), which have been documented in

some rivers of the British Columbia coast via escapes from aquaculture net pens (Amos

and Appleby, 1999). All other fish species caught, including forage fish, will also be

identified and enumerated.

This literature review, habitat inventory, and study plan provides a foundation for

our sampling effort in the Grays Harbor Estuary. The literature review focuses on the

primary literature concerning juvenile salmonid use of estuaries, as well as a section on


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the literature specific to the Grays Harbor estuary and riverine tidal waters. The review

summarizes both peer-reviewed journal articles and non peer-reviewed “grey literature”

(WDFW technical reports, DOE, etc.). The habitat inventory documents the type and

spatial distribution of the various intertidal habitats found in the Grays Harbor estuary,

and compares current distribution and abundance to historical conditions. Both the

literature review and habitat inventory are fundamental to developing a robust sampling

plan that builds upon the findings of previous studies and the current distribution of

intertidal habitats in the Grays Harbor estuary.


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Literature Review

The Role of Estuaries in the Life History of Juvenile Salmon:

An estuary is broadly defined as “a semi-enclosed coastal body of water with a

free connection to the open ocean in which salt water is diluted with runoff from the

land” (Pritchard, 1967). Over the last century, estuaries received a gradual increase in

attention for their role in sustaining Pacific salmonid abundance and diversity. Initially,

the prevailing thought was that ocean and estuary habitats were essentially limitless, and

that density-dependent factors in fresh water were the major determinants in regulating

salmon populations. As the importance of factors beyond fresh water habitats began to

be appreciated (beginning in the 1950’s), estuaries then became viewed as “bottlenecks”

to salmon production (i.e. limiting factors), and studies were carried out to determine the

effect of bypassing estuaries by releasing hatchery produced salmon directly into marine

waters (Bottom et al., 2005b). However, these studies failed to show an increase in adult

salmon abundance, and as salmon populations in the Pacific Northwest continued to

decline, researchers again reconsidered the prevailing paradigm. Estuarine research

intensified in the 1960’s, and that work has shaped our current understanding: “the

estuary has come to be regarded as part of the continuum of ecosystems that salmon

need to utilize in order to complete their life cycle, rather than a place that salmon need

to avoid” (Fresh et al., 2005).

Although estuarine dependence and residence times differ among salmonid

species, the identification of diverse life history types both within and between various

species was pivotal in promoting our understanding of the importance of estuaries.

Reimers (1973) identified five chinook salmon life history types in the Sixes River (OR),

and scale analysis indicated that fish with the longest estuarine residence times

contributed 90% of the adult spawning population. Other studies, conducted from

northern California to southeast Alaska, have also shown that estuarine residence is


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beneficial for juveniles and eventual adult recruitment of chinook salmon (Neilson et al.,

1985; Macdonald et al., 1988; Levings et al., 1989; Sommer et al., 2001; Magnusson and

Hilborn, 2003; Bottom et al., 2005a; Greene et al., 2005) and coho salmon (Solazzi et al.,

1991; Linley, 2001; Magnusson and Hilborn, 2003). The life histories of pink and chum

salmon, which tend to emigrate directly to sea after emergence, makes these two species

less dependent on estuary residence, although in some systems chum salmon may

spend up to two months in the estuary (Thorpe, 1994). The connection between

estuarine use by juvenile steelhead and adult returns has not been as well-studied, but a

report by Ward and Slaney (1990) found that residence in the Keogh River estuary (B.C.)

did not significantly improve hatchery steelhead survival over fresh water habitats;

steelhead released directly into the marine environment also had similar returns.

However, steelhead residing in a small coastal lagoon estuary in California had high

growth rates and made up a majority of the eventual marine emigrants in comparison

with those rearing in fresh water (Hayes et al., 2008).

Estuaries have been shown to enhance the survival of juvenile salmon by

providing:

(1) habitat for overwintering juvenile salmonids forced downstream during

high river flows (Simenstad et al., 1992; Sommer et al., 2001; Henning et al.,

2007);

(2) complex low-velocity refugia such as off-channel sloughs and large

woody debris (LWD) (Simenstad et al., 1981; Gonor et al., 1988; Swales and

Levings, 1989; Wick, 2002; Henning et al., 2006; 2007; Hering et al., 2010);

(3) time for migrating juveniles to adapt physiologically to sea water (Folmar

and Dickhoff, 1980; Healey, 1980; Levy and Northcote, 1982; Iwata and

Komatsu, 1984; Zaugg et al., 1985);

(4) opportune feeding conditions as drift insects and other prey items are

trapped and concentrated due to flow reversals (Simenstad and Eggers,

1981; Tschaplinski, 1987; Eggleston et al., 1998);


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(5) settling of suspended sediments and detritus, which can fuel soft-

sediment habitat formation and detritus-based food webs exploited by

salmon (Simenstad et al., 1982; Thorpe, 1994; Bottom et al., 2005b; Maier and

Simenstad, 2009).

(6) a refuge from piscivorous and avian predators, due in part to the often

turbid water resulting from river flows and tidal action (Simenstad et al., 1982;

Thorpe, 1994; Gregory and Levings, 1998; De Robertis et al., 2003).

Temporal Estuarine Habitat Usage:

The major environmental cue for juvenile chinook and coho salmon, particularly

those of wild origin, to enter higher salinity estuarine water is thought to be the lunar

apogee, when tidal influences are minimal (DeVries et al., 2004), although for other

species, river flows, photoperiod, and nocturnal illumination may also be involved

(Mason, 1975; Durkin, 1982). In general, smaller salmonids (age 0+, “ocean type”, or

subyearlings) tend to spend more time in estuarine waters and are thus more dependent

on estuarine habitats than larger juveniles (age 1+, “stream type”, or yearlings), which

typically reside in streams for their first year of life prior to smolting. The following table,

based on Fresh et al. (2005), summarizes these trends for juvenile salmon in the

Columbia River estuary; the pattern is similar for other estuaries in the Pacific Northwest.


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Table 1: Temporal Habitat Use Patterns of Juvenile Pacific salmon in the

Columbia Estuary:

Species Stream Type (Yearlings)

Coho salmon

Some Chinook populations

Steelhead

Sockeye salmon

Ocean Type (Subyearlings)

Coho Salmon

Some Chinook populations

Chum salmon

Pink salmon

Attributes Longer period of fresh water

rearing (>1 year)

Shorter ocean residence

Short period of estuarine

residence

Larger size at estuarine entry

Short period of fresh water

rearing

Longer ocean residence

Longer period of estuarine

residence (except pink salmon)

Smaller size at estuarine entry

[Note: in the following sections, sockeye and pink salmon estuarine behavior will not be

covered because these species are not present in Grays Harbor watersheds]

Once in the estuary, habitat usage is largely dictated by life history (time of entry)

and fish size, although there are limited data available for some of the less common life

history strategies. The timing of entry into the estuary may also influence the length of

estuarine residence; Beamer et al. (2005) found that early migrating chinook salmon fry

in the Skagit River marsh/delta use a different suite of habitats than fish migrating later

in the year. Given that juvenile chinook salmon are present in the Skagit River system

from February through October, different life history strategies appear to have adapted

to seasonal changes in flow/inundation and foraging opportunities. There is also


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evidence that wild chinook salmon juveniles have longer estuarine residence times in

comparison with hatchery origin fish (Levings et al., 1986; Beamer et al., 2005), which

may be due to the tendency for hatchery fish to be released at larger sizes. Chinook

salmon also have the greatest degree of documented life history variation, with

residence times ranging from a few weeks to several months (Levy and Northcote, 1982;

Simenstad et al., 1982; Thorpe, 1994; Beamer et al., 2005; Bottom et al., 2005a; Hering et

al., 2010). Coho salmon typically enter the estuary as yearlings after rearing in fresh

water for one year, with residence times ranging on scales from days to weeks (common)

up to three months (rare) (Durkin, 1982; Healey, 1982; Thorpe, 1994). However, coho

salmon also have diverse life histories and migration patterns that vary by region of

origin (Weitkamp et al., 2000). The majority of coho salmon yearlings emigrate to sea,

but in Puget Sound, some may remain throughout the summer and mature, returning to

rivers in the fall as precocious “jacks” (Simenstad et al., 1982). However, an alternative

life history, the coho salmon “nomad”, may enter estuaries as subyearlings and spend the

entire summer (mainly in shallow intertidal habitats) there before returning to fresh

water to overwinter, emigrating to sea the following year (Koski, 2009). A recent study

by Chittenden et al. (2008) used acoustic tagging to show that wild coho salmon

juveniles in the Campbell River system (British Columbia) spent less time in the estuary

than hatchery reared smolts, though estuary rearing was important for both. Chum

salmon also have a variety of life history strategies with; mark – recapture studies

showed a range from 1.7 - 4 days in the Skagit River marsh to 2 - 3 months in the

Yaquina River estuary (Oregon) (Healey, 1982; Thorpe, 1994). There is also evidence that

residence times vary by season of emigration, perhaps as a result of changes in

flow/inundation and differing prey availability (Simenstad et al., 1982).

Spatial Estuarine Habitat Usage:

Chinook salmon are the most well-studied species, and several reports indicate

that subyearlings are more common in shallow water habitats, entering tidal channels

and flats during periods of high flows and flooding tides (Healey, 1980; Zaugg et al.,


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1985; Levings et al., 1991; Fresh et al., 2005). However, a recent report suggests that

subyearling chinook salmon habitat usage is diverse, and fish may enter tidal channels

even during ebbing tides, despite the increased stranding risk (Hering et al., 2010).

Yearling chinook salmon tend to reside in deeper dendritic tidal or river channels (Zaugg

et al., 1985; Thorpe, 1994; Bottom et al., 2005a), and demonstrate a preference for

eelgrass beds, which may afford protection from predators (Semmens, 2008). Juvenile

coho estuary habitat use is varied and may include both shallow tidal channels and

borders and deeper channel boundaries, with larger individuals preferring deeper

habitats (Healey, 1982; Zaugg et al., 1985; Moser et al., 1991). Juvenile chum salmon

enter estuaries soon after emerging from redds and reside in shallow habitats initially,

utilizing tidally inundated channels (Mason, 1974; Macdonald and Chang, 1993). Chum

salmon exit these channels late in the tidal dewatering stage, similar to juvenile chinook

salmon (Levy and Northcote, 1982), although their behavior may be complex, with some

individuals entering tidal channels during ebbing tides (Mason, 1974). They appear to be

restricted to the fresh water “lens” at the top of the water column until they can adjust to

sea water (Iwata and Komatsu, 1984). After acclimating (in as little as 24 hours), they

may disperse to habitats with a broad range of salinities several times per day (Mason,

1974; Iwata and Komatsu, 1984).

Study Area Overview:

Grays Harbor (the Chehalis River estuary) is the second largest estuary in the state

of Washington after the Columbia River estuary. The Grays Harbor estuary is a bar-built

estuary that was formed by the combined processes of sedimentation and erosion

caused by both the Chehalis River and the Pacific Ocean (Chehalis Basin HWG, 2010).

The estuary covers 23,504 hectares at mean high high-water (MHHW) from the mouth at

Westport to Montesano, and encompasses the tidally influences lower reaches of the

Chehalis, Humptulips, Hoquiam, Wishkah, Johns and Elk Rivers as well as several smaller


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tributaries. The total drainage area, including all of the above tributaries, is 660,450

hectares, with 79% of the fresh water input from the Chehalis River (Simenstad and

Eggers, 1981). The system flows are rainfall driven, with peak flows from December-

January in an average year, and minimal input from snowmelt in the southern Olympic

Mountains (surface drainage occurs primarily through the Satsop River basin). In the

upper estuary (“Inner Harbor”), the main river channel splits into north and south

channels; the north channel has been dredged for navigation. Vertical salinity

stratification, with a salt water wedge typical of estuarine systems, occurs only in the

south channel (Simenstad and Eggers, 1981).

Land use in the immediate vicinity of the estuary was historically dominated by

surge plain ecosystems (Chehalis Basin HWG, 2010). Vegetation in the intertidal region

was dominated by dense eel grass beds. The primary factor determining riparian land

cover was the vertical distance above the average high tide line; plant communities

nearest the average high tide line were comprised of salt tolerant species, and the

presence of salt tolerant species decreased with increasing vertical distance from the

high tide line (Chehalis Basin HWG, 2010).

Between 1900 and 1980, the Grays Harbor estuary had an overall net decrease in

tidal wetlands due to extensive diking and filling activities, particularly in the upper

portions of the estuary (Boule et al., 1983). A more recent analysis of historical estuarine

habitat change detailed a 22% decline in tidal flats (3,493 hectares) due to upland

conversion at the mouth of Grays Harbor and along the north channel, an increase in

potential eelgrass habitat (1,793 hectares), and an increase in areas below extreme low-

water (ELW) (409 hectares), mainly due to a deepening of the channel near the mouth of

the estuary (Borde et al., 2003). Upland logging may have led to an increase in sediment

transport to the estuary, resulting in loss of tidal flats due to increased elevation.

Dredging for navigation has dramatically deepened the area near the mouth of the

estuary, as well as along the north channel, resulting in changes in circulation; wakes


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from large vessels may have increased channel border erosion and loss of tidal flats in

the southern area of the estuary. Historically, the estuary received sediment input from

the Columbia River, but the construction of jetties (first in 1900, then in the 1930s) may

have reduced this input, which may also explain the loss of tidal flats in the lower estuary.

(Borde et al., 2003). The northern part of the estuary (“North Bay”) has experienced little

change.

Although much of the basin has been degraded by a combination of logging,

channelization, gravel mining, water diversion, road building, diking, dredging,

aquaculture, small-scale coal mining, mill effluent, sewage release and pesticide use for

aquaculture and cranberry farming (Hiss et al., 1982; Smith and Wenger, 2001; Wood and

Stark, 2002) , the area of the lower mainstem Chehalis River (river km 1-17, just east of

Aberdeen to the confluence of the Wynoochee River), contains high-quality rearing

habitat for juvenile salmon, particularly coho, and has been well studied (Moser et al.,

1991; Simenstad et al., 1992; Miller and Simenstad, 1997; Henning et al., 2006; 2007) .

The area contains numerous sloughs and tidal channels, a relatively undeveloped

floodplain with seasonal inundation, and a riparian forest dominated by older stands of

conifers and hardwoods (Ralph et al., 1994).

Salmonid Species Distributions and Estuarine Use - Chehalis River Estuary:

“Within the Chehalis region, we have numerous distinct stocks of salmonids that are

important to the overall biological diversity in Washington State. These include one stock

of spring chinook, one stock of summer chinook, seven stocks of fall chinook, two stocks

of fall chum, seven stocks of coho salmon, two stocks of summer steelhead, and eight

stocks of winter steelhead (WDFW and WWTIT 1994). In addition, cutthroat trout are

found throughout the drainage, and bull trout have been documented as present, but

specific distribution data do not exist” (Smith and Wenger, 2001).

1) Chinook salmon: Although there are two runs (spring and fall chinook salmon)

present in Chehalis River basin (Deschamps et al., 1970), there are very few


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reports of yearlings (offspring of the spring run chinook salmon) being captured

in the estuary. There is strong consensus among the earlier reports for the run

timing of subyearlings (fall chinook): in the lower Chehalis River main stem,

subyearlings were captured from late January through June (peaking in April),

and were absent by late July through September (Deschamps et al., 1970; Tokar

et al., 1970; Brix, 1981). In the estuary (most studies focused on the upper estuary

and areas along the northern navigation channel), subyearlings were captured

from January through November (Tokar et al., 1970; Simenstad and Eggers, 1981),

with the peak catches occurring during May (Deschamps et al., 1970) or mid-

June (Brix, 1974; 1981). Juvenile chinook were captured in both the north and

south channels of the upper estuary (Simenstad and Eggers, 1981). Although

catches of juvenile chinook declined rapidly after June, there is evidence that

juveniles are present throughout the estuary nearly year-round (Simenstad and

Eggers, 1981), although only one of the studies sampled continuously throughout

the year (Tokar et al., 1970). This suggests a variety of chinook salmon life

histories are present in the basin, and, particularly for wild chinook, estuarine

residence times are longer than for other salmonid species. There appears to be

limited production of chinook from the southern tributaries (Elk and Johns Rivers)

(Simenstad and Eggers, 1981). Most of these studies utilized beach seines for

sampling, and this method was found to result in higher catches per-unit-effort

(CPUE) than purse seining.

2) Coho salmon: In the lower main stem Chehalis River, yearling coho salmon

were captured from early February through June, peaking in mid-April to mid-

May, at which point they emigrate out of the system (Wright, 1973; Brix, 1974),

though for yearling coho, this was apparently a function of hatchery release

timing (Brix, 1981). Some larger coho were captured that were in their third year

(by scale analysis), again suggesting multiple life histories within the basin


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(Deschamps et al., 1970). Studies of subyearling coho reported captures from

March through October, peaking in mid-April through mid-June (Tokar et al.,

1970; Brix, 1974; Moser et al., 1991). In the upper estuary, catches peaked from

mid-April to June 1st, with the highest CPUE around Cow Point. Catches in the

lower estuary increased 1-2 months later, peaking June 9-27th, indicating a period

of estuarine residence, although the size frequencies of upper and lower estuary

catches were similar (100-170 mm) (Tokar et al., 1970; Simenstad and Eggers,

1981). This may be due to different sources of juvenile coho, i.e. Humptulips

River versus Chehalis River (see below). Most of the sampling effort in these

studies was conducted using beach seines, although Simenstad and Eggers

(1981) reported roughly equal CPUE by beach seining and purse seining. In

contrast, Schroder and Fresh (1992), who also used beach and purse seines,

found that beach seining consistently caught more salmon (and fewer baitfish)

than purse seining, and noted “…the purse seine was difficult to use because of

sunken debris and the high current and windy conditions that often prevailed in

the harbor” (page 133).

Two studies gathered information on emigration/residence times in the Chehalis

River basin using acoustic tags (Moser et al., 1991; Schroder and Fresh, 1992) and

coded-wire tags (CWT) (Schroder and Fresh, 1992). Both reported that juvenile

coho of hatchery origin moved downstream quickly in the Chehalis River (average

of 3.1 km/day) (Moser et al., 1991), independent of size at release or water

temperature, but their migration slowed in the estuary. Coho did not move

directly seaward with river and tidal currents, but instead swam against strong

ebbing flows to remain in the estuary, suggesting estuarine residence may be

important to allow completion of smolting (salt water adaptation), feeding and

growth, source water imprinting, or reduced predation (Moser et al., 1991).

Juvenile coho residency was estimated at 5 days in the upper estuary/inner

harbor area (near Cow Point), with fish seeking areas of reduced currents


16

(channel boundaries, etc.) and structure (i.e. pilings and docks); some fish

probably reside in this area for “several weeks” (Schroder and Fresh, 1992).

Overall, subyearling coho reside in the estuary up to several months and are

mostly absent by June (though some were captured as late as October), and thus

spend less time in the estuary than juvenile chinook salmon (Simenstad and

Eggers, 1981). Juvenile coho were present in all tributaries of Grays Harbor and

utilized both the north and south channels in the upper estuary (for stocks

originating from the Chehalis River), though the north channel was slightly

preferred. This was notable because, at the time of the study, the Weyerhaeuser

mill released 48-50 million gallons of effluent per day into the south channel,

which was (along with lesser effluents from the ITT - Rayonier mill) identified as

contributing to the poor survival of fish originating from the Chehalis River and

tributaries (Schroder and Fresh, 1992).

Coho salmon are the most well studied salmonid species in the Grays Harbor

basin. The study by Schroder and Fresh (1992), designed to investigate the much

higher survival of hatchery coho salmon released in the Humptulips River versus

those of the same stock released from the Satsop/Chehalis Rivers, found that

coho originating from the Humptulips River behaved differently than those from

other tributaries of the Grays Harbor estuary. Of 220,000 CWT coho smolts

released from the Humptulips River hatchery in the study, only 5 were recovered

in North Bay during an extensive beach seining effort 10 days later –

electroshocking surveys in the lower Humptulips River were also negative,

providing evidence that these fish exited the area quickly. In addition, very few of

the coho released from the Humptulips River were captured in the upper estuary

at any time, and they were thought to have resided in South Bay (Chehalis river

estuary) or emigrated to sea (Schroder and Fresh, 1992). The study concluded

that poor water quality caused by mill effluents (toxic chemicals and suspended

solids with a high biological oxygen demand, which lowered the dissolved


17

oxygen content of downstream estuarine waters), coupled with infection by

Nanophyetus salmincola (a trematode infection that is much more common in

the Chehalis basin than in the Humptulips River), were identified as the main

causes for the differences in survival.

3) Chum salmon: Emigration of juvenile chum salmon in the lower mainstem

Chehalis River begins as early as January (Deschamps et al., 1970), and is certainly

underway by late February and early March. Juvenile chum (chum salmon

emigrate as subyearlings; (Healey, 1982) were captured in large numbers from

mid-March to mid-May in several studies, peaking in mid-April (Tokar et al.,

1970; Wright, 1973; Brix, 1974; 1981; Simenstad and Eggers, 1981). In the upper

estuary, the CPUE for chum salmon peaked in early March at Cow Point; at

Westport (lower estuary) the CPUE peaked in late April, and chum were found to

utilize both the north and south channels (Simenstad and Eggers, 1981). Capture

of juvenile chum salmon was typically by beach seine, and in those studies using

both beach and purse seines, beach seining accounted for the majority of the

catch (Simenstad and Eggers, 1981; Schroder and Fresh, 1992). By late May, most

juvenile chum have exited the estuary and gone to sea, a typical estuarine use

pattern for this species (Mason, 1974; Iwata and Komatsu, 1984; Quinn, 2005).

The average period of estuarine residency for chum was estimated at 2-4 weeks

by Simenstad and Eggers (1981), based on mark – recapture efforts. As such,

juvenile chum salmon rely on estuarine residence much less than either chinook

or coho salmon.

4) Steelhead trout: Juvenile steelhead, which may emigrate to sea at between

one and three years of age (Quinn, 2005), were present in the Grays Harbor

estuary from April to late July (Tokar et al., 1970) and were taken in roughly equal

numbers by beach and purse seines (Simenstad and Eggers, 1981). Steelhead

were captured in both the upper and lower estuary, but overall, very few (<11)


18

were captured in any of the previous studies despite concentrated seining efforts

(Tokar et al., 1970; Brix, 1974; Simenstad and Eggers, 1981). Previous experience

in the Columbia River estuary showed that steelhead smolts tended to utilize the

deeper, faster channels to emigrate, possibly explaining the low numbers taken

by beach seining (unpublished data, L. Weitkamp, NOAA).

5) Cutthroat Trout: cutthroat trout of any age class (i.e. juvenile or adult) were

rarely captured in the Grays Harbor estuary in previous field studies. Deschamps

et al. (1970) noted some juveniles were caught in the upper estuary from early

March through September, but too few were captured to identify a peak

migration period. Wright (1973) reported that juvenile cutthroat trout reared in

the lower reaches of the mainstem Chehalis and Satsop Rivers year-round, and

that adults were found throughout the Chehalis River basin. Extensive sampling

by beach and purse seines resulted in the capture of only two cutthroat (164 mm

and 196 mm) in the study conducted by Simenstad and Eggers (Simenstad and

Eggers, 1981). Tokar et al. (1970) captured a total of nine cutthroat during two

years of continuous seining, mainly from March-May, but noted “It is probable

that many cutthroat remain in the north channel and outer harbor for their entire

lives, making periodic movements into fresh water for feeding and spawning”

(page 6). Sea run adults were first captured in July and remained in the estuary

through September, though in small numbers (Wright, 1973).

6) Bull Trout/Dolly Varden: Bull trout were also extremely uncommon in all of

the previous Chehalis River basin studies. The few bull trout captured were taken

by beach seining in the lower mainstem Chehalis River (near Cosmopolis) and

both the upper and lower Grays Harbor estuary (Tokar et al., 1970; Wright, 1973;

Simenstad and Eggers, 1981). Some early reports questioned the existence of

spawning stocks in the Chehalis River Basin, and suggested that any bull trout


19

present were strays from more robust populations in Olympic Peninsula rivers

such as the Queets and Hoh (Deschamps et al., 1970). As of 2004, the

Washington Department of Fish and Wildlife classified bull trout in the Chehalis

River and Grays Harbor estuary as a distinct stock based on geographic

distribution, but there is no information on spawning locations or timing within

the basin (WDFW, 2004). The WDFW currently manages bull trout and Dolly

Varden (S. malma) as one group, “native char”, due to a lack of genetic stock

analysis to separate the species. In 2006, the ACOE contracted (R2 Resource

consultants) a study of native char in the lower Chehalis River and upper Grays

Harbor estuary to determine if channel dredging operations might negatively

affect populations in the Chehalis River estuary. Using the same size beach seine

net as in Simenstad and Eggers (1981), they conducted 784 seines at sites

between the mouth of the Hoquiam River and Cosmopolis, capturing 15 native

char between mid-March and mid-June (2001-’04) (Jeanes and Morello, 2006).

Seven of these were marked with external anchor tags and implanted with

acoustic transmitters in 2003-’04, and subsequent receiver detections revealed

that char may be present in Grays Harbor from February-mid July. Notably, two

of the tagged fish were later caught by steelhead anglers in the Hoh River, more

than 80 miles to the North. None of the tagged fish ventured into the upper

Chehalis River, and the study concluded that “Unlike the Skagit River

[populations], native char do not appear to spawn in the Chehalis River basin and

probably originate in the Olympic Coast rivers” (page 57) (Jeanes and Morello,

2006), supporting the work of Deschamps et al. (1970). Although fin clips were

taken for genetic analysis to determine if the char captured in the study were bull

trout or Dolly Varden, no results were reported (Jeanes and Morello, 2006). At

present it is thought that Dolly Varden populations, where present, are restricted

to waters upstream of anadromous barriers, and that all native char residing in

anadromous zones are bull trout (Jeanes and Morello cite a personal


20

communication from M. Downen, WDFW). As a result of the study, the ACOE has

shifted the in-water work window for dredging to July 15 through February 15 in

an attempt to avoid impacting native char in the lower Chehalis River. It should

be noted, however, that other species of anadromous salmonids (particularly

juvenile Chinook salmon) are present in the Grays Harbor estuary during that

time period.

Non-Salmonid/Baitfish Distributions and Estuarine Use:

The primary source for information concerning baitfish abundance and

distribution in the Grays Harbor estuary is by Simenstad and Eggers(1981), the only study

to also specifically target baitfish populations in the estuary. They reported 8 baitfish

species commonly captured, primarily via purse seining. The most common of these was

the northern anchovy (Engraulis mordax), present from mid-May through late

September, with larval and adult stages having a “ubiquitous distribution” in the estuary.

The second most common species encountered was Pacific herring (Clupea harengus),

with juveniles consistently captured from mid-June through September, particularly in

the lower estuary where salinities were highest. There was strong evidence of estuarine

spawning and rearing, with spawning thought to occur near eelgrass beds, although

attempts to gather herring eggs by raking eelgrass beds were largely unsuccessful.

English sole (Parophrys vetulus) were present throughout the study period (March to

October), and two age classes were detected. Yearling sole (130 – 150 mm) were

captured early in the year near deeper channels, while young-of-the-year sole were

found in shallow waters after March. English sole larvae were reported to have settled

out in the estuary after a period of pelagic residence in nearshore marine waters from

March through May. Three species of smelt were also captured. Juvenile longfin smelt

(Spirinchus thaleichthys) were the most common and were captured in upper estuary

sites, present throughout the study. Influxes occurred in March, mid-May to mid-July,


21

and mid-August through September, and there was some evidence of estuarine

spawning and rearing. Surf smelt (Hypomesus pretiosus) were caught primarily at lower

estuary sites and were less common, although when captures occurred surf smelt were

very abundant (CPUE >50 fish/set). Whitebait smelt (Allosmerus elongatus) were also

caught, though infrequently. [There was no mention of eulachon (the Columbia River

smelt, Thaleichthys pacificus), which is presently under consideration for protection under

the ESA, being captured in the study.] The final two species were American shad (Alosa

sapidissima), found in low abundance at upper estuary sites, and Pacific sand lance

(Ammodytes hexapterus), which were infrequently captured, though present in high

abundance when detected.

An earlier study (Tokar et al., 1970), targeting salmonids, also reported seine

catches of the following species: 3-spine stickleback (Gasterosteus aculeatus), Pacific

snakeblenny (Snake Prickleback? Lumpenus sagitta), white perch (Morone americana),

pile perch (Rhacochilus vacca), shiner perch (Cymatogaster aggregate), starry flounder

(Platichthys stellatus), sand sole (Psettichthys mealnostictus), Staghorn sculpin

(Leptocottus armatus), prickly sculpin (Cottus asper), peamouth (Mylocheilus caurinus),

bay pipefish (Syngnathus leptorhynchus), lamprey (Pacific? Lampetra tridentata), northern

squawfish (now known as the northern pikeminnow, Ptychocheilus oregonensis), sucker

(no species given), Pacific Tomcod (Microgadus proximus), rockfish (no species given),

saddleback gunnel (Pholis ornata), and hagfish (Pacific? Eptatretus stoutii).

Wright (1973), also using a beach seine, reported catches of these additional

species in tidal waters: largescale sucker (Catastomus macrocheilus), spiny dogfish

(Squalus acanthias) , red-tail surf perch (Amphistichus rhodoterus), arrow goby

(Clevelandia ios), kelp greenling (Hexagrammos decagrammus), and Pacific sanddab

(Citharichthys sordidus). [Scientific names from (Miller and Lea, 1972) and

www.fishbase.org ]


22

Habitat Inventory

The intertidal areas of the Grays Harbor estuary were divided into six zones:

mouth of the estuary, central estuary, North Bay, South Bay, upper estuary (referred to in

the literature as the “inner harbor”), and Chehalis River surge plain (see Figure 1). The

habitat classification was done using a geographic information systems (GIS) database

developed for that purpose. The National Wetlands Inventory (NWI) GIS database was

used as a basis for our classification (USFWS, 2010). The NWI classes were used to group

the polygons into subtidal, intertidal, emergent wetlands, shrub/scrub, and forested

classes. Then soil data, Shore Zone Inventory data from the Washington Department of

Natural Resources (DNR) (2001), and 2009 aerial imagery (USDA, 2009) were used to

categorize the intertidal polygons into aquatic vegetation bed, mud flat, sand flat, and

beach classes. During this step a comprehensive field inspection of the classification

result was conducted to verify the accuracy and make corrections as needed. Finally, the

Shore Zone Inventory data (WADNR, 2001) were used to delineate some preliminary

eelgrass habitats (a specific type of aquatic vegetation bed) (Figure 1). WFC will map

additional locations of eelgrass habitat in the Grays Harbor estuary during the summer

when flows and turbidity decrease, allowing field identification and coordinate fixing via

GPS. As a result, we expect some of the habitats currently categorized as aquatic

vegetation beds to change to eelgrass in the final report.

The acreage of each habitat type, by zone, is shown in Table 2, below. These

data were used to guide our choices of sampling sites; areas of open water were

excluded (although in some cases we are sampling the channel margins of some of these

areas, which are typically aquatic vegetation beds or sand flats). Mud flats in North Bay

and the central estuary must be sampled during low tides, when the exposed areas

provide a barrier against which the net is drawn, allowing fish to become entrapped. The

flats could be sampled by purse seining, which does not require solid ground for

entrapment, but the high quantities of large woody debris in the mud flats are a constant


23

source of snags, making sampling of shallow areas via purse seine extremely difficult

(Kurt Fresh and Bob Burkle, personal communication; see also (Schroder and Fresh,

1992)). Previous studies working in Grays Harbor also reported that purse seines were

less effective at catching juvenile salmon than beach seines (Simenstad and Eggers,

1981). For this reason, we have minimal coverage of mud flats in the sampling plan (see

Table 3 for a breakdown of habitat acreage with open water and mud flats removed).

Our efforts in these areas will therefore focus on sampling aquatic vegetation beds,

adjacent to the mud flats. A breakdown of our proposed sampling sites, broken out by

zone and habitat type, is provided in Table 4. Table 5 shows the percentage of each

habitat type covered by all of the proposed sampling sites, and Table 6 shows the

habitat coverage for the primary sites only (for both, open water and mud flats

excluded).


24

Figure 1: Habitat Types and Proposed Grays Harbor Estuary Sampling Sites


25

Table 2: Summary of Grays Harbor intertidal habitat types by zone (in acres):

Table 3: Grays Harbor intertidal habitat types by estuary zone – Open water and mud flats removed (in acres):

Habitat Type Mouth Central Inner North Bay South Bay Surge Plain Grand Total % of Grand

Total Open Water/Channel 2,826.06 11,694.93 2,860.62 2,283.65 1,444.27 1,599.32 22,708.85 30.68 Aquatic Vegetation Bed 53.06 7,456.73 105.91 7,133.70 3,834.21 0 18,583.61 25.10 Eelgrass 0 15.62 90.47 0 138.72 0 244.81 0.33 Mud Flat 0 3,664.91 4,199.87 5,657.43 756.69 0 14,278.89 19.29 Sand Flat 0 2,626.21 166.60 0 674.61 0 3,467.42 4.68 Cobble/Gravel/Sand Beach 141.46 211.86 0 0 0 0 353.33 0.48 High Emergent Marsh 223.53 387.08 678.99 815.36 2,789.97 832.04 5,726.97 7.74 Scrub/Shrub Cover 38.19 77.61 1,086.87 269.38 326.72 784.97 2,583.74 3.49 Forested 0 8.33 1,386.03 390.35 341.31 3,950.23 6,076.25 8.21

Total 3,282.31 26,143.28 10,575.36 16,549.86 10,306.49 7,166.56 74,023.87

Habitat Type Mouth Central Inner North Bay South Bay Surge Plain Grand Total % of Grand

Total Open Water/Channel Aquatic Bed 53.06 7,456.73 105.91 7,133.70 3,834.21 0 18,583.61 50.18 Eelgrass 0 15.62 90.47 0 138.72 0 244.81 0.66 Mud Flat 0 Sand Flat 0 2,626.21 166.60 0 674.61 0 3,467.42 9.36 Cobble/Gravel/Sand Beach 141.46 211.86 0 0 0 0 353.33 0.95 High Emergent Marsh 223.53 387.08 678.99 815.36 2,789.97 832.04 5,726.97 15.46 Scrub/Shrub Cover 38.19 77.61 1,086.87 269.38 326.72 784.97 2,583.74 6.98 Forested 0 8.33 1,386.03 390.35 341.31 3,950.23 6,076.25 16.41

Total 456.25 10,783.44 3,514.87 8,608.78 8,105.54 5,567.24 37,036.13


26

Table 4: Proposed sampling sites (primary sites are in bold font), by

zone:

Site name Zone Habitat Type Sampling Gear

Point Brown marsh Mouth High Emergent Marsh Seine

Westport (ocean side) Mouth Cobble/Gravel/Sand Beach Seine

South Bay Channel South Bay Eelgrass Seine

Elk River Flats South Bay Forested Seine

Beardslee Slough South Bay Aquatic Vegetation Bed Seine

Mallard Slough South Bay High Emergent Marsh Fyke Net

John's River channel South Bay High Emergent Marsh Seine

John's River slough South Bay High Emergent Marsh Fyke net

Ocean Shores Flats North Bay Aquatic Vegetation Bed Seine

North Bay Flats North Bay Aquatic Vegetation Bed Seine

Cambpell Slough North Bay Scrub/Shrub Cover Fyke Net

Humptulips River mouth North Bay Aquatic Vegetation Bed Seine

Chinois Creek Flats North Bay Aquatic Vegetation Bed Seine

Grass Creek North Bay High Emergent Marsh Fyke Net

Sand Island channel Central estuary Aquatic Vegetation Bed Seine

Sand Island Flats Central estuary Aquatic Vegetation Bed Seine

Goose Island Flats Central estuary Aquatic Vegetation Bed Seine

Damon Point Central estuary Cobble/Gravel/Sand Beach Seine

Bar off John's River Central estuary Aquatic Vegetation Bed Seine

Stearn's Bluff Central estuary Aquatic Vegetation Bed Seine

Moon Island Upper estuary Aquatic Vegetation Bed Seine

Rennie Island Upper estuary Sand Flat Seine

Cow Point Upper estuary High Emergent Marsh Seine

Little Hoquiam River Upper estuary Scrub/Shrub Cover Seine

Hoquiam River Upper estuary Forested Seine

E. Fork Hoquiam slough Upper estuary Scrub/Shrub Cover Fyke Net

East Fork Hoquiam River Upper estuary Forested Seine

Lower Wishkah River Upper estuary Forested Seine

Wishkah River Upper estuary Scrub/Shrub Cover Fyke Net

South Channel Upper estuary Aquatic Vegetation Bed Seine

Charlie Creek Upper estuary High Emergent Marsh Fyke Net

Elliot Slough Surge Plain High Emergent Marsh Seine

Preacher's Slough Surge Plain Forested Seine

Sand Island East Surge Plain High Emergent Marsh Seine

Upper surge plain Surge Plain Scrub/Shrub Cover Seine

Chehalis River surge plain Surge Plain Forested Fyke Net


27

Table 5: Sampling site habitats, by percentage (open water and mud flats

excluded):

Table 6: Primary site habitats, by percentage (open water and mud flats

excluded):

All Sites by Habitat Coverage: Count Percentage

Open Water/Channel 0 0

Aquatic Vegetation Bed 12 33.33

Eelgrass 1 2.78

Mud Flat 0 0

Sand Flat 1 2.78

Cobble/Gravel/Sand Beach 2 5.56

High Emergent Marsh 9 25.00

Scrub/Shrub Cover 5 13.89

Forested 6 16.67

Total 36

Primary Site Habitat Coverage Count Percentage

Open Water/Channel 0 0

Aquatic Vegetation Bed 11 42.31

Eelgrass 1 3.85

Mud Flat 0 0

Sand Flat 1 3.85

Cobble/Gravel/Sand Beach 1 3.85

High Emergent Marsh 5 19.23

Scrub/Shrub Cover 2 7.69

Forested 5 19.23

Total 26


28

Study Plan

Study Objective:

Provide a scientific basis for the selection and prioritization of future salmonid

habitat restoration and protection projects within the Grays Harbor estuary.

Study Goals:

Calculate the amount of each habitat type in the Grays Harbor estuary using a

GIS to ensure that we are sampling each type representatively (complete, except

for eelgrass beds)

Determine the relative abundance, distribution and emigration timing of juvenile

salmonids in the Grays Harbor estuary and tidally-influenced portions of its

major tributaries

Gather information on the distribution, abundance and community structure of

non-salmonid fishes in these same areas

Use the capture of coded wire tagged salmonids to identify basin of origin, infer

estuarine residence times, and estimate emigration speeds and growth following

release

Establish sampling continuity with previous studies in the Grays Harbor estuary

(Simenstad and Eggers, 1981; Schroder and Fresh, 1992; Jeanes and Morello,

2006) by sampling at Cow Point (upper estuary), Rennie Island (upper estuary),

Moon Island (upper/central estuary), North Bay, and Sand Island (surge plain) to

determine if fish habitat usage has changed over time as water quality has

improved in the estuary


29

Specific Hypotheses:

There is differential use of estuarine habitat type by juvenile salmonids in the Grays

Harbor estuary.

Juvenile salmon utilize certain intertidal habitats in greater numbers than would be

predicted by the abundance of those habitats within the greater habitat matrix of

the Grays Harbor estuary (habitat selectivity).

Juvenile salmon from upstream tributaries will utilize habitats in South Bay (Johns

and Elk River estuaries), even though natural production in these systems is low.

Few smolts emigrating the Humptulips River will utilize “upstream” habitat (East of

the Humptulips River delta), instead travelling to areas in South Bay or directly to

sea (as reported by Schroder and Fresh) (1992).

Eelgrass beds will have higher densities of juvenile salmon, based on the results of

previous research (Thom, 1993; Thorpe, 1994).

2011 Sampling Plan:

It has been over 20 years since the last comprehensive juvenile salmon sampling

effort took place in the Grays Harbor estuary. Previous research was typically driven by

a specific problem, e.g. sampling near the north channel was performed to determine

the effects of channel dredging for navigation, as in Simenstad and Eggers (1981). We

will use some of the sites from previous projects to establish a sampling continuity that

will help us better understand the present habitat usage of juvenile fish in the estuary, as

well as providing a historical context that may indicate important trends or data gaps.


30

However, this project will encompass a wider variety of sites and habitat types than in

previous work, including the lower tidal portions of several tributaries.

To ensure coverage of the 6 zones and various habitat types, we propose a two-

tier sampling system consisting of primary sites (N=26; these are in bold font, Table 4),

sampled bi-weekly, and additional secondary sites (N= 10) sampled less frequently (with

a goal of at least once per month). In total, we will sample at approximately 36 sites

from March-September of 2011; some of these sites, particularly those in the estuary

mouth, will be sampled less frequently as tides and weather permit. Sample sites have

been selected to ensure a representative distribution in space and habitat type to ensure

that we are capturing the appropriate range of potential habitat usage (specific locations

and GPS coordinates forthcoming).

At some sites, sampling will be done by conducting boat-based beach seine

hauls that will be replicated through time, within sites. At least two hauls will be made at

each site to provide a measure of catch variability. The general locations of these sites

are: Point Brown marsh, Westport (ocean side of harbor), South Bay channel, Elk River

flats, Beardslee Slough, John’s River channel, Ocean Shores Flats, North Bay flats,

Humptulips River mouth, Chinois Creek flats, Sand Island Channel (central estuary), Sand

Island flats, Goose Island flats, Damon Point, Bar off of John’s River, Stearn’s Bluff, Moon

Island, Rennie Island, Cow Point, Little Hoquiam River, Hoquiam River, East Fork Hoquiam

River, Lower Wishkah River, South Channel, Elliot Slough, Preacher’s Slough (surge plain),

Sand Island East (a different “Sand Island”, in the surge plain), Upper surge plain (a total

of 28 sites) (Table 4).

Additionally , we will sample some shallow water sites using fyke nets deployed

at high tide and fished through the ebb. The general locations of these sites are: Charlie

Creek , Wishkah River, East Fork Hoquiam River slough, Grass Creek, Campbell Slough,

Mallard Slough (off of the Elk River channel), John’s River slough, Chehalis surge plain (a

total of 8 sites) (Table 4).


31

All fish captured will be enumerated, identified to species, and visually scanned

for marks and tags (all hatchery-origin salmon in the system are reportedly tagged or

clipped- Bob Burkle, WDFW). Juvenile salmonids will also be scanned for coded wire

tags (CWT), and a sub-sample of tagged salmon will be kept in order to determine basin

of origin and release date. The first 20 individuals of each species captured at a site will

be measured for fork length. At each site we will collect basic water quality parameters

such as temperature, salinity, and dissolved oxygen. For each beach seine and fyke net

sets, the area of habitat sampled will be calculated. This will allow us to normalize our

catch data by area, allowing statistical comparisons between sampling sites.


32

Sampling Permits

The only salmonid species in the Chehalis River estuary currently under

protection by the ESA is the bull trout (threatened). Based on the literature review of

previous work (above), we expect to encounter very few bull trout, but capture remains a

possibility. Therefore, we have applied (January, 2011) for a sampling permit from the

regional U.S. Fish and Wildlife Service office. A copy of the permit application is available

upon request.

A WDFW Scientific Collection Permit is required for this study. WFC has this

permit in-hand, and a copy is available upon request.


33

References BIBLIOGRAPHY

Amos, K. H. & Appleby, A. (1999). Atlantic salmon in Washington state: A fish management perspective. p. 13. Olympia: Washington Department of Fish and Wildlife. Beamer, E., McBride, A., Greene, C. M., Henderson, R., Hood, G., Wolf, K., Larsen, K., Rice, C. & Fresh, K. (2005). Delta and nearshore restoration for the recovery of wild Skagit River Chinook salmon: Linking estuary restoration to wild Chinook salmon populations. p. 97. LaConner, WA: Skagit River System Cooperative. Borde, A. B., Thom, R. M., Rumrill, S. & Miller, L. M. (2003). Geospatial habitat change analysis in Pacific Northwest Coastal estuaries. Estuaries 26, 1104-1116. Bottom, D. L., Jones, K. K., Cornwell, T. J., Gray, A. & Simenstad, C. A. (2005a). Patterns of Chinook salmon migration and residency in the Salmon River estuary (Oregon). Estuarine, Coastal and Shelf Science 64, 79-93. Bottom, D. L., Simenstad, C. A., Burke, J., Baptista, A. M., Jay, D. A., Jones, K. K., Casillas, E. & Schiewe, M. H. (2005b). Salmon at River's End: The role of the estuary in the decline and recovery of Columbia River salmon. p. 246: U.S. Department of Commerce, NOAA technical memo, NMFS-NWFSC-68. Boule, M. E., Olmsted, N. & Miller, T. (1983). Inventory of wetland resources and evaluation of wetland management in Western Washington. Olympia: Washington State Department of Ecology, prepared by Shapiro and Associates, Seattle. Brix, R. (1974). 1973 Studies of juvenile salmonids in rivers tributary to Grays Harbor, Washington. p. 51. Olympia: Washington Department of Fisheries. Brix, R. (1981). Data report of Grays Harbor juvenile salmon seining program, 1973 - 1980. p. 77. Olympia: Washington Department of Fisheries. Chittenden, C. M., Sura, S., Butterworth, K. G., Cubitt, K. F., Manel-La, N. P., Balfry, S., Okland, F. & McKinley, R. S. (2008). Riverine, estuarine and marine migratory behaviour and physiology of wild and hatchery-reared coho salmon Oncorhynchus kisutch (Walbaum) smolts descending the Campbell River, BC, Canada. Journal of Fish Biology 72, 614-628. De Robertis, A., Ryer, C. H., Veloza, A. & Brodeur, R. D. (2003). Differential effects of turbidity on prey consumption of piscivorous and planktivorous fish. Canadian Journal of Fisheries and Aquatic Sciences 60, 1517-1526. Deschamps, G., Wright, S. G. & Watson, R. E. (1970). Fish migration and distribution in the lower Chehalis River and upper Grays Harbor. (Fisheries, W. D. o., ed.), pp. 1-59. Olympia. DeVries, P., Goetz, F., Fresh, K. & Seiler, D. (2004). Evidence of a lunar gravitation cue on timing of estuarine entry by Pacific salmon smolts. Transactions of the American Fisheries Society 133, 1379-1395. Durkin, J. T. (1982). Migration characteristics of coho salmon (Oncorhynchus kisutch) smolts in the Columbia River and its estuary. In Estuarine Comparisons (Kennedy, V. S., ed.), pp. 365-376. New York: Academic Press. Eggleston, D. B., Armstrong, D. A., Elis, W. E. & Patton, W. S. (1998). Estuarine fronts as conduits for larval transport: hydrodynamics and spatial distribution of Dungeness crab postlarvae. Marine Ecology-Progress Series 164, 73-82.


34

Folmar, L. C. & Dickhoff, W. W. (1980). The parr-smolt transformation (smoltification) and seawater adaptation in salmonids. Aquaculture 21, 1-37. Fresh, K., Casillas, E., Johnson, L. & Bottom, D. L. (2005). Role of the estuary in the recovery of Columbia River basin salmon and steelhead: An evaluation of the effects of selected factors on salmonid population viability. p. 125. Seattle: Northwest Fisheries Science Center, NOAA. Gonor, J. J., Sedell, J. R. & Benner, P. A. (1988). What we know about large trees in estuaries, in the sea, and on coastal beaches. In From the forest to the sea: a story of fallen trees (Maser, C., Tarrant, R. F., Trappe, J. M. & Franklin, J. F., eds.), pp. 83-112. Portland, OR: U.S. Forest Service, Pacific Northwest Research Station. Greene, C. M., Jensen, D. W., Pess, G. R. & Steel, E. A. (2005). Effects of environmental conditions during stream, estuary, and ocean residency on Chinook salmon return rates in the Skagit River, Washington. Transactions of the American Fisheries Society 134, 1562-1581. Gregory, R. S. & Levings, C. D. (1998). Turbidity reduces predation on migrating juvenile Pacific salmon. Transactions of the American Fisheries Society 127, 275-285. Hayes, S. A., Bond, M. H., Hanson, C. V., Freund, E. V., Smith, J. J., Anderson, E. C., Ammann, A. J. & Macfarlane, R. B. (2008). Steelhead growth in a small central California watershed: Upstream and estuarine rearing patterns. Transactions of the American Fisheries Society 137, 114-128. Healey, M. C. (1980). Utilization of the Nanaimo River estuary by juvenile Chinook salmon, Oncorhynchus tshawystcha. Fishery Bulletin 79, 653-668. Healey, M. C. (1982). Juvenile Pacific salmon in estuaries: The life support system. In Estuarine Comparisons (Kennedy, V. S., ed.), pp. 315-342. New York: Academic Press. Henning, J. A., Gresswell, R. E. & Fleming, I. A. (2006). Juvenile salmonid use of freshwater emergent wetlands in the floodplain and its implications for conservation management. North American Journal of Fisheries Management 26, 367-376. Henning, J. A., Gresswell, R. E. & Fleming, I. A. (2007). Use of seasonal freshwater wetlands by fishes in a temperate river floodplain. Journal of Fish Biology 71, 476-492. Hering, D. K., Bottom, D. L., Prentice, E. F., Jones, K. K. & Fleming, I. A. (2010). Tidal movements and residency of subyearling Chinook salmon (Oncorhynchus tshawytscha) in an Oregon salt marsh channel. Canadian Journal of Fisheries and Aquatic Sciences 67, 524-533. Hiss, J., Meyer, J. & Boomer, R. (1982). Status of Chehalis River salmon and steelhead fisheries and problems affecting the Chehalis Tribe. p. 61. Olympia: U.S. Fish and Wildlife Service. Iwata, M. & Komatsu, S. (1984). Importance of estuarine residence for adaptation of chum salmon (Oncorhynchus keta) fry to seawater. Canadian Journal of Fisheries and Aquatic Sciences 41, 744-749. Jeanes, E. D. & Morello, C. M. (2006). Native char utilization: Lower Chehalis River and Grays Harbor Estuary, Aberdeen, Washington. p. 81. Redmond, WA: U.S. Army Corps of Engineers. Koski, K. V. (2009). The fate of coho salmon nomads: The story of an estuarine-rearing strategy promoting resilience. Ecology and Society 14. Levings, C. D., Conlin, K. & Raymond, B. (1991). Intertidal habitats used by juvenile Chinook salmon (Oncorhynchus-tshawytscha) rearing in the north arm of the Fraser-River estuary. Marine Pollution Bulletin 22, 20-26. Levings, C. D., McAllister, C. D. & Chang, B. D. (1986). Differential use of the Campbell River estuary, British-Columbia, by wild and hatchery-reared juvenile Chinook salmon (Oncorhynchus-tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences 43, 1386-1397. Levings, C. D., McAllister, C. D., MacDonald, J. S., Brown, T. J., Kotyk, M. S. & Kask, B. A. (1989). Chinook salmon and estuarine habitat: A transfer experiment can help evaluate estuarine


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dependency. In Proceedings of the special workshop on effects of habitat alteration on salmonid stocks (Levings, C. D., Holtby, L. B. & Henderson, M. A., eds.), pp. 116-122. Ottawa: Canadian Special Publication of Fisheries and Aquatic Sciences. Levy, D. A. & Northcote, T. G. (1982). Juvenile salmon residency in a marsh area of the Fraser River estuary. Canadian Journal of Fisheries and Aquatic Sciences 39, 270-276. Linley, T. J. (2001). Influence of short-term estuarine rearing on the ocean survival and size at return of coho salmon in southeastern Alaska. North American Journal of Aquaculture 63, 306-311. Macdonald, J. S. & Chang, B. D. (1993). Seasonal use by fish of nearshore areas in an urbanized coastal inlet in southwestern British Columbia. Northwest Science 67, 63-77. Macdonald, J. S., Levings, C. D., McAllister, C. D., Fagerlund, U. H. M. & McBride, J. R. (1988). A field experiment to test the importance of estuaries for Chinook salmon (Oncorhynchus tshawytscha) survival- short term results. Canadian Journal of Fisheries and Aquatic Sciences 45, 1366-1377. Magnusson, A. & Hilborn, R. (2003). Estuarine influence on survival rates of Coho (Oncorhynchus kisutch) and Chinook salmon (Oncorhynchus tshawytscha) released from hatcheries on the US Pacific Coast. Estuaries 26, 1094-1103. Maier, G. O. & Simenstad, C. A. (2009). The Role of Marsh-Derived Macrodetritus to the Food Webs of Juvenile Chinook Salmon in a Large Altered Estuary. Estuaries and Coasts 32, 984-998. Mason, J. C. (1974). Behavioral ecology of chum salmon fry in a small estuary. Journal of the Fisheries Research Board of Canada 31, 83-92. Mason, J. C. (1975). Seaward movement of juvenile fishes, including lunar periodicity in movement of coho salmon (Onchorhynchus kisutch) fry. Journal of the Fisheries Research Board of Canada 32, 2542-2547. Miller, D. J. & Lea, R. N. (1972). Guide to the coastal marine fishes of California. Oakland: University of California. Miller, J. A. & Simenstad, C. A. (1997). A comparative assessment of a natural and created estuarine slough as rearing habitat for juvenile Chinook and coho salmon. Estuaries 20, 792-806. Moser, M. L., Olson, A. F. & Quinn, T. P. (1991). Riverine and estuarine migratory behavior of coho salmon (Oncorhynchus kisutch) smolts. Canadian Journal of Fisheries and Aquatic Sciences 48, 1670-1678. Neilson, J. D., Geen, G. H. & Bottom, D. (1985). Estuarine growth of juvenile Chinook salmon (Oncorhynchus tshawytscha) as inferred from otilith microstructure. Canadian Journal of Fisheries and Aquatic Sciences 42, 899-908. Pritchard, D. W. (1967). What is an estuary? Physical viewpoint. In Estuaries (Lauff, H., ed.), pp. 3-5. Washington, DC: American Association for the Advancement of Science. Quinn, T. P. (2005). The behavior and ecology of Pacific salmon and trout. Bethesda, Maryland: American Fisheries Society and the University of Washington Press. Ralph, S. C., Peterson, N. P. & Mendoza, C. C. (1994). An inventory of off-channel habitat of the lower Chehalis River with applications of remote sensing. Lacey, WA: U.S. Fish and Wildlife, prepared by Natural Resource Consultants, Inc. Reimers, P. E. (1973). The length of residence of juvenile fall Chinook salmon in the Sixes River, Oregon. p. 42. Portland, OR: Fish Commission of Oregon. Schroder, S. & Fresh, K. (1992). Results of the Grays Harbor coho survival investigations, 1987-1990. p. 413. Olympia: Washington Department of Fisheries.


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Semmens, B. X. (2008). Acoustically derived fine-scale behaviors of juvenile Chinook salmon (Oncorhynchus tshawytscha) associated with intertidal benthic habitats in an estuary. Canadian Journal of Fisheries and Aquatic Sciences 65, 2053-2062. Simenstad, C. A., Cordell, J. R., Hood, W. C., Miller, J. A. & Thom, R. M. (1992). Ecological status of a created estuarine slough in the Chehalis River estuary: report of monitoring in created and natural estuarine sloughs. Seattle: Army Corps of Engineers. Simenstad, C. A. & Eggers, D. M. (1981). Juvenile salmonid and baitfish distribution, abundance, and prey resources in selected areas of Grays Harbor, Washington. Seattle, WA: University of Washington, Fisheries Research Institute. Simenstad, C. A., Fresh, K. L. & Salo, E. O. (1981). The role of Puget Sound and Washington coastal estuaries in the life history of Pacific Salmon- An unappreciated function. Estuaries 4, 285-286. Simenstad, C. A., Fresh, K. L. & Salo, E. O. (1982). The role of Puget Sound and Washington coastal estuaries in the life history of Pacific salmon: An unappreciated function. In Estuarine Comparisons (Kennedy, V. S., ed.), pp. 343-364. New York: Academic Press. Smith, C. J. & Wenger, M. (2001). Salmon and Steelhead habitat limiting factors: Chehalis basin and nearby drainages, WRIA 22 and 23. p. 448. Lacey, WA: Washington State Conservation Commission. Solazzi, M. F., Nickelson, T. E. & Johnson, S. L. (1991). Survival, contribution, and return of hatchery coho salmon (Oncorhynchus-kisutch) released into fresh-water, estuarine, and marine environments. Canadian Journal of Fisheries and Aquatic Sciences 48, 248-253. Sommer, T. R., Nobriga, M. L., Harrell, W. C., Batham, W. & Kimmerer, W. J. (2001). Floodplain rearing of juvenile chinook salmon: evidence of enhanced growth and survival. Canadian Journal of Fisheries and Aquatic Sciences 58, 325-333. Swales, S. & Levings, C. D. (1989). Role of off-channel ponds in the life-cycle of coho salmon (Oncorhynchus-kisutch) and other juvenile salmonids in the Coldwater River, British Columbia. Canadian Journal of Fisheries and Aquatic Sciences 46, 232-242. Thom, R. M. (1993). Eelgrass (Zostera marina L.) transplant monitoring in Grays Harbor, Washington, after 29 months. p. 21. Richland, WA: Pacific Northwest Laboratory. Thorpe, J. E. (1994). Salmonid fishes and the estuarine environment. Estuaries 17, 76-93. Tokar, E. M., Tollefson, R. & Denison, J. G. (1970). Grays Harbor: downstream migrant salmonid study. p. 93. Shelton, WA: ITT-Rayonier, Inc. Olympic Research Division. Tschaplinski, P. J. (1987). The use of esturies as rearing habitats by juvenile coho salmon. In Applying 15 years of Carnation Creek Results (Chamberlin, T. W., ed.), pp. 123-141. Nanaimo, B.C.: Pacific Biological Station. USDA (2009). NAIP Aerial Imagery. National Agriculture Imagery Program, U.S. Department of Agriculture. USFWS (2010). Classification of Wetlands and Deepwater Habitats of the United States. U.S. Fish and Wildlfie Service. WADNR (2001). Washington State shorezone inventory. Washington State Department of Natural Resources, Nearshore Habitat Program. Ward, B. R. & Slaney, P. A. (1990). Returns of pen-reared steelhead from riverine, estuarine, and marine releases. Transactions of the American Fisheries Society 119, 492-499. WDFW (2004). Washington State Salmonid Stock Inventory: Bull Trout/Dolly Varden. p. 449. Olympia: Washington Department of Fish and Wildlife.


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Weitkamp, L., Wainwright, T. C., Bryant, G. J., Teel, D. J. & Kope, R. G. (2000). Review of the status of coho salmon from Washington, Oregon, and California. Sustainable Fisheries Management: Pacific Salmon, 111-118. Wick, A. J. (2002). Ecological function and spatial dynamics of large woody debris in oligohaline brackish estuarine sloughs for juvenile Pacific salmon. In School of Aquatic and Fisheries Sciences, p. 125. Seattle: University of Washington. Wood, B. & Stark, J. D. (2002). Acute toxicity of drainage ditch water from a Washington state cranberry-growing region to Daphnia pulex in laboratory bioassays. Ecotoxicology and Environmental Safety 53, 273-280. Wright, S. G. (1973). Resident and anadromous fishes of the Chehalis and Satsop Rivers in the vicinity of Washington public power supply system's proposed nuclear project no.3. p. 26. Olympia: Washington Department of Fisheries. Zaugg, W. S., Prentice, E. F. & Waknitz, F. W. (1985). Importance of river migration to the development of seawater tolerance in Columbia River anadromous salmonids. Aquaculture 51, 33-47.

Documents

Grays Harbor Juvenile Fish Use Assessment, Literature Review