Grays Harbor Juvenile Fish Use Assessment, Literature Review

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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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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.

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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);

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

(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.

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

Table 1: Temporal Habitat Use Patterns of Juvenile Pacific salmon in the Columbia Estuary: Species Stream Type (Yearlings) Ocean Type (Subyearlings)

Coho salmon Coho Salmon

Some Chinook populations Some Chinook populations

Steelhead Chum salmon

Sockeye salmon Pink salmon

Attributes Longer period of fresh water Short period of fresh water rearing (>1 year) rearing

Shorter ocean residence Longer ocean residence

Short period of estuarine Longer period of estuarine residence residence (except pink salmon)

Larger size at estuarine entry 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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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.,

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

(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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

(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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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)

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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,

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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 ]

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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).

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

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

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

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

Table 5: Sampling 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

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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.

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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).

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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.

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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.

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

References BIBLIOGRAPHY

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Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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.

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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.

Grays Harbor Juvenile Fish Use Assessment: Project Introduction

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.