PRIMARY RESEARCH PAPER

Fish habitat use response to anthropogenic induced changesof physical processes in the Elwha estuary, Washington,USA

J. Anne Shaffer • M. Beirne • T. Ritchie •

R. Paradis • D. Barry • P. Crain

Received: 5 February 2009 / Revised: 2 September 2009 / Accepted: 11 September 2009 / Published online: 19 October 2009

� Springer Science+Business Media B.V. 2009

Abstract The Elwha River estuary has been signif-

icantly influenced by anthropogenic changes to the

river, including two large dams upriver and rock

dikes installed in the estuary. Together these have

disrupted hydrodynamic processes and subsequent

sediment delivery throughout the watershed. This

article defines the functional response of fish distri-

bution within the estuary as a result of these changes.

We assessed fish distribution of three main areas of

the Elwha estuary using standard beach seining

techniques from March to August 2007. Species

composition, ecological indices, and relative propor-

tion of all salmonids, and in particular Chinook

salmon (Oncorhynchus tshawytscha), were consis-

tently significantly different across the estuary. Dif-

ferences corresponded to a rock dike installed

30 years ago, and a sediment lens that was observed

to form at the entrance to the east estuary. Sediment

lenses are documented to be a common occurrence in

the Elwha nearshore, and symptomatic of docu-

mented, severely disrupted sediment processes of the

Elwha River. Combining the fish distribution docu-

mented in this study with the rock dike and observed

sediment lens and the sediment processes docu-

mented by other researchers we, therefore, conclude:

(1) Fish use within the Elwha River estuary is

complex, and even fragments of connected estuary

are critically important for migrating salmon; (2)

Anthropogenic effects, including in river damming

and diking of the estuary, can be an important

ecological driver in nearshore habitat function that

should be appropriately considered in estuary habitat

research, management, and restoration; and (3)

Juvenile salmonids appear to be able to respond to

dynamic sediment environments if there are habitat

options available.

Keywords Nearshore � Estuary � Sediment �Hydrodynamics � Salmon � Chinook � Elwha � Habitat

Handling editor: Pierluigi Viaroli

J. A. Shaffer (&) � T. Ritchie

Washington Department of Fish and Wildlife,

332 E. 5th Street, Port Angeles, WA 98362, USA

e-mail: anne.shaffer@dfw.wa.gov

M. Beirne

Lower Elwha Klallam Tribe, Fish Hatchery Road,

Port Angeles, WA 98362, USA

e-mail: matt.beirne@elwha.nsn.us

R. Paradis � D. Barry

Western Washington University, Huxley College of the

Environment, Port Angeles, WA 98362, USA

e-mail: Rebecca@clallambroadband.com

D. Barry

e-mail: dwight.barry@wwu.edu

P. Crain

Olympic National Park, 600 Park Avenue, Port Angeles,

WA 98362, USA

e-mail: Patrick_crain@nps.gov

123

Hydrobiologia (2009) 636:179–190

DOI 10.1007/s10750-009-9947-x

Introduction

Hydrodynamic processes, including channel morphol-

ogy and sediment delivery, define estuarine habitat

form (Marshall & Elliot, 1998; Williams et al., 2002).

Hydrodynamic processes can result in significant

impacts to habitat function and fish population

dynamics. For example, Gregory (1993) and Gregory

& Levings (1998) found that turbidity defined preda-

tion success by juvenile Chinook in the Fraser River,

and Hood (2002) documented the importance of

hydrodynamic flow in habitat utilization in estuaries.

Sediment delivery is another component of estuarine

hydrodynamics that forms nearshore habitats.

Although an important component of estuarine hydro-

dynamics, less is known about the role that sediment

delivery plays in estuarine habitat function for fish.

Similarly, human alterations, including diking and

filling of nearshore environments, can significantly

disrupt hydrodynamic processes and, as a result,

habitat function (Hood, 2004; Toft et al., 2007).

Located on the north Olympic Peninsula in Wash-

ington state, USA, the Elwha River supports no fewer

than three federally listed salmon (Winter & Crain,

2008). The Elwha estuary, which connects the Elwha

watershed with the Strait of Juan de Fuca, is a

classified a dynamic stream delta estuary that is

defined by high-energy riverine and marine processes

(Todd et al., 2006). The current estuary is relatively

small, and includes approximately 90 acres of tidal

channel estuary. Prior to the early 1900s, the Elwha

estuary was much larger, more diverse structurally,

and included complex tidal channels and distributaries

as well as tidal lagoons. The river mouth was dynamic,

and defined by shifting sand bars that formed offshore

at the river mouth (Todd et al., 2006).

The Elwha estuary has been hydromorphologically

disrupted by two anthropogenic events:

(1) Two hydroelectric dams installed in the

watershed have resulted in approximately

100 years of sediment starvation throughout the

lower watershed and nearshore areas. The dams

are both managed as run-of-the-river and do not

regulate water flow, but have severely disrupted

sediment processes by inhibiting transport of sand

and gravel sediment to the lower river. Disruption

of sediment delivery has had a number of effects

on the hydrodynamics of the lower river and

estuary of the Elwha (Draut et al., 2008). Conse-

quently the estuary is now much smaller and less

complex, and has a smaller, foreshortened, and

unstable river mouth and tidal lagoon area. The

Elwha lower river that bisects the estuary is much

more channelized, and has repeatedly migrated

laterally to the east and west over the last 67 years

(Draut et al., 2008; Todd et al., 2006). Although

not quantified, ephemeral sediment bars/lenses

continue to form at the mouth (Lower Elwha

Klallam Tribe, pers obs.; Todd et al., 2006).

(2) An earthen and rock dike along the west estuary

installed in the 1960s has resulted in a truncated

and functionally disconnected estuary; that has

disconnected approximately one-third of the west

estuary from the rest of the lower river habitat and

continues to modify riverine flow patterns.

The current Elwha estuary can be split into three

sections that are at the same tidal elevation and

connection to the Strait shoreline: (1) The east

estuary, located east of the river mouth, which

includes approximately 63 acres (71% of the total

estuary); (2) The west estuary, which includes 18

acres of habitat (19% of the total estuary), which is

connected directly to the west Elwha river mouth on

its east side, and is bordered to the west by a rock

levee; and (3) The impounded estuary, which

includes 9 acres (10% of total estuary) of estuary,

and is separated from the unimpounded west estuary

by the dike. This west levee creates a total fish barrier

between the river and the impounded estuary (Fig. 1).

The Elwha River watershed is slated to undergo a

large-scale restoration event via the removal of two

large hydroelectric dams that were installed in the

river over a 100 years ago and that have severely

disrupted the sediment processes of the Elwha River.

Damming has had a significant impact on the Elwha

River ecosystem, including increasing the erosion of

the river bed, a decrease in recruitment of gravels

needed to create suitable habitats for spawning,

which have been trapped in the sediment load behind

the dams, and an increase in water temperature which

negatively impacts fish spawning and rearing. A

special edition of Northwest Science has been

dedicated to the science and restoration of the Elwha

watershed (Duda et al., 2008).

Dam removal is slated to begin in 2011 (Winter &

Crain, 2008), and will result in the transport of

180 Hydrobiologia (2009) 636:179–190

123

approximately 1.5–2.3 million m3 of coarse (sand and

gravel) sediment and (4–5 million m3) of fine (sand/

silt) sediment from the upper river to the nearshore,

including the Elwha estuary, within 5 years of dam

removal (Randle et al., 2004).

Given the critical importance of estuarine systems

for juvenile fish survival (Beamer et al., 2003, 2005;

Fresh, 2006), the historic importance of the Elwha

watershed to federally listed salmon species, and the

large scale restoration that is to occur, understanding

how the Elwha estuary functions is central to defining

and understanding the full ecosystem recovery (Shaffer

et al., 2008). At present, very little is known about basic

fish distribution of the Elwha estuary. The Washington

Department of Fish and Wildlife and the Lower Elwha

Klallam Tribe, with numerous partners including

Western Washington University and Peninsula Col-

lege, have therefore begun monitoring fish distribution

of the Elwha estuary to assess habitat function. In this

study, we attempt to understand fish distribution of the

three areas of the Elwha estuary and, if different,

identify what role the physical processes that have been

disrupted by anthropogenic features of sediment

starvation and diking may play in fish distribution.

We also define the next priority steps in ecosystem

monitoring, management, and restoration.

Methods and materials

We define habitat function based on fish distribution

as reflected by various ecological indices, including

diversity, abundance, and morphological metrics. Our

hypotheses for this study are as follows:

H01 Species diversity is not significantly different

between impounded, west, and east portions of the

Elwha estuary;

H02 Total fish and salmon abundance is not signif-

icantly different between impounded, west, and east

portions of the Elwha estuary, and;

H03 Fish length for major salmon species is not

significantly different between east and west estuary.

S T R A I T O F J U A N D E F U C AS T R A I T O F J U A N D E F U C A

Elwha River Main Channel

Elwha River Main Channel

ImpoundedWest Estuary

4.1 ha.

EastEstuary28.5 ha.

West Estuary8.7 ha.

0 200100

Meters

1996 Shoreline

LEKT Reservation

2001 LiDaR Elevation (ft.)

�2 � 4

5 � 10

11 � 15

16 � 25

26 � 1,304

Lower Elwha Klallam Tribal G.I.S. Dept.Map prepared by: Randall E. McCoy

Elwha River Estuary 09 (hydrobiologia).mxd

Location MapLocation Map

Project SiteProject Site

WashingtonState

WashingtonState

Fig. 1 Map of the Elwha Estuary with elevational profile and the three sampling areas delinated. Asterisks indicate sample sites

Hydrobiologia (2009) 636:179–190 181

123

The east, west, and impounded areas of the Elwha

estuary were sampled using standard beach seining

methodology during the salmon outmigration period

(March–August) 2007. Large and small Puget Sound

Protocol (PSP) nets were used in the west estuary.

The large PSP seine net was used in the east estuary.

A total of 4–6 seines were conducted across the three

stations of the east estuary every other week. A total

of 1–2 seines were conducted along the west estuary

weekly. Two seines were conducted in the

impounded estuary weekly. By the end of May,

dense accumulations of green algal mats in the

impounded estuary made the area unworkable, and

potentially unsafe for human health. The impounded

portion of the west estuary was therefore only

sampled during March–May 2007. During each

sampling, all the fish in the net were identified to

the lowest possible taxa and counted. The first

twenty-five individuals of each species were mea-

sured in both fork and total fish length and recorded

in millimeters. Species richness and Shannon–Wiener

diversity (H0) indices were calculated (Zar, 1984) for

each month, and for each portion of the estuary.

ANOVA and t-tests were used to evaluate differ-

ences in study variables between the three estuary

areas using the coin package (Hothorn et al., 2008) in

the R system for statistical computing (ver. 2.8.0, R

Development Core Team, 2008) and RT4Win soft-

ware (Huo et al., 2006). Monte Carlo simulation with

10,000 replications was used to generate approximate

P-values for ANOVAs and systematic permutation

was used to generate exact P-values for t-tests

(Edgington & Onghena, 2007). Also using R, Welch’s

correction for the t-distribution was used to obtain 95%

confidence intervals on means as well as the differ-

ences between means. Percent similarity indices were

calculated to compare sites by evaluating the density

of each species that occurred in at least one site with

the other two sites. For each species, the lowest

relative species density value is selected, and the sum

of those species density percentages among sites

reflects the degree of similarity among sites (McCune

et al., 2002).

Results

A total of 118 seines were conducted from March to

August 2007 (Table 1). Salmon, particularly Chinook

(Oncorhynchus tshawytscha), coho (O. kisutch),

chum (O. keta), cutthroat (Salmo clarki clarki), and

steelhead (Salmo gairdneri), smelt (primarily Hy-

pomesus pretiousus pretiousus), threespine stickle-

back (Gasterosteus aculeatus), and staghorn sculpin

(Leptocottus armatus) were the dominant fish species

collected (Tables 2, 3). Fish species composition

varied in each area. Ecological indices and individual

species densities also varied by month, with higher

densities and diversities observed during June, July,

and August (Figs. 2, 3; Tables 4, 5). In total, 47% of

the fish were collected in the west estuary. Over 90%

of juvenile salmonids (all species) and 94% of

juvenile Chinook salmon were collected in the west

estuary (Tables 2, 4). The total number of fish

collected in the impounded estuary was comparable

to the other sites in March and April, and had the

highest percentage of fish in May. However, the

species composition of the impounded estuary dif-

fered from that of the east and west estuary. Juvenile

salmonids were not collected in the impounded

estuary, which was instead dominated by large

populations of three spine sticklebacks.

Species diversity (F = 10.338, P = 0.004) and

richness (F = 19.513, P = 0.0001) were statistically

different between the three sites (Fig. 2; Table 6).

The west estuary had the highest values for all the

indices. In general, the greatest differences in diver-

sity and richness were between the west estuary and

the impounded estuary, followed by the east and west

estuary. Percent similarity analysis indicated the

greatest similarity between the east and impounded

estuary, and the lowest similarity between the west

and impounded estuary (Table 7).

Frequency of occurrence of all the fish species

combined was not significantly different among the

three sites (Fig. 2). Densities of Chinook, coho, and

Table 1 Seining summary Elwha estuary 2007

Date Number of Seines by site Total

East West Impounded

March 10 2 2 14

April 12 6 6 24

May 15 6 10 31

June 8 6 ns 14

July 10 8 ns 18

August 4 5 ns 9

182 Hydrobiologia (2009) 636:179–190

123

chum salmon were all significantly greater in the west

estuary than in the other areas of the Elwha estuary

(Fig. 4; Table 4).

Body length of salmonids among sites was vari-

able. Chum and Chinook length increased during the

sampling season. Cutthroat, steelhead, and coho

lengths generally remained consistent. Lengths for

Chinook and chum differed significantly by month

(Fig. 4a, b). Fish lengths for all the species differed

significantly between east and west portions of the

estuary (P \ 0.001).

Discussion

Fish distribution within the Elwha estuary reflects

complexity in fish life history and habitat. Fish

abundance varied through the season, corresponding

with salmon outmigration in the east and west estuary,

and strong seasonal reproduction of non-migrating

species (sculpin and sticklebacks) primarily in the

impounded and east estuary. Salmon outmigration

observed during this study includes both wild and in-

river hatchery releases of coho, Chinook, and steel-

head. Changes in salmon lengths over the sampling

period reflect growth of fish during the season.

Surprisingly, mean coho size did not increase during

the sampling period, likely due to hatchery supple-

mentation (Crain et al., pers obs.).

Statistical analysis of ecological indices and fish

metrics led us to reject all three of our null hypotheses

and conclude that the three areas of the Elwha estuary

appear to be functioning differently for fish. Percent

similarity results reveal that the east and impounded

areas of the estuary exhibited relatively more similar

ecological characteristics than the connected east and

west estuaries. The difference in Chinook and chum

densities of the east and west estuary was also found to

be biologically statistically significant, with more fish

present on the west than the east estuary.

Given the similarities in tidal elevation, proximity

to shoreline and river, and lack of other habitat

alterations of the three areas, the functional differ-

ences between the three areas of the Elwha estuary

are likely due to anthropogenic events that result in

physical obstructions to fish movement in two ways.

First, fish access to the impounded portion of the

Elwha estuary has been obstructed for decades by the

permanent dike, which is a complete fish passage

barrier, resulting in a much different fish assemblage

than observed in portions of the estuary that migrat-

ing fish can access. Second, sediment bars or lens are

a common feature offshore of the Elwha River mouth

as documented in historic accounts (Todd et al.,

2006). One such sediment lens was observed, but not

quantified, to have formed in the lower river at the

entrance to the east estuary at or just prior to the

beginning of the annual juvenile salmon outmigration

period in 2007 (Lower Elwha Klallam Tribe pers

obs.). This lens is believed to have disrupted fish

Table 2 Percent summary of dominant fish collected from Elwha estuary

Site 3-Spine

stickleback

Chinook Coho Chum Cut throat Steelhead Smelt Starry

flounder

Staghorn

sculpin

Cottids

Impounded 100 0 0 0 0 0 0 0 0 0

East 82 3 1 0 0 1 0 3 6 3

West 40 25 4 2 1 0 0 6 8 11

Table 3 Percentage of all fish collected in east, west, and

impounded areas of Elwha estuary by month

Percent of total fish

East

estuary

West

estuary

Impounded Total

Date

March 27 33 40 100

April 27 39 34 100

May 7 19 75 100

June 38 62 ns 100

July 27 73 ns 100

August 48 52 ns 100

Total percent

March–May 11 23 66 100

June–August 41 59 ns 100

All months 32 47 21 100

Note that owing to sampling limitations, the impounded

estuary was sampled during March–May only

Hydrobiologia (2009) 636:179–190 183

123

184 Hydrobiologia (2009) 636:179–190

123

access to the east estuary during, at least, part of our

study. In contrast to these two areas, the west portion

of the Elwha estuary experienced no blockages to fish

access, and as a result reflected a more diverse

estuarine ecosystem with respect to fish diversity and

abundance than the impounded area (literally only

meters away), and the east estuary.

While we were not able to quantify the sediment bar

formation during this study, previous studies by others

that documents variation in sediment delivery to the

lower Elwha River support the idea that the sedimen-

tation lens disrupted fish access to the east estuary.

Between September 2006 and April 2007, the lower

0.5 km of the river channel, including the area of our

study, migrated eastward approximately 10 m, and the

river bed aggraded by as much as 1 m with sand and

gravel deposits (Draut et al., 2007). There is also a

large body of evidence that supports our conclusion of

sedimentation being a driving factor in fish distribu-

tion of the estuary. Sediment processes in the Elwha

River are documented to be significantly disrupted,

and large scale sediment starvation has changed the

hydrodynamic processes of the lower river, causing

large seasonal changes in the river bed (Draut et al.,

2008; Randle et al., 2004). Disruption of physical

processes has played a dominant role in Elwha lower

river and nearshore habitat (Draut et al., 2008; Warrick

et al., 2008; Warrick et al., 2009). Unconstrained, low

gradient channel reaches in the lower Elwha River

historically contained extensive side channels (Pess

et al., 2008) and estuarine slack-water habitats with

suitable substrate for critical fish distribution, includ-

ing eulachon spawning. Truncation of sediment

transport to the lower river, along with channelization

and the systematic removal of large woody debris

(LWD), has caused channel incision and an increase in

bed substrate size (Pohl, 2004). Nearshore effects of

this disruption likely include a significant reduction in

Table 4 Difference in mean densities of salmonids between

the east and west estuaries (fish/m3 ± 95% CI)

Species Difference

(fish/m3 ± 95% CI)

t P

Chinook 0.2127 ± 0.1047 3.36 0.001

Coho 0.0307 ± 0.0278 1.91 0.05

Chum 0.0131 ± 0.0118 1.94 0.04

Table 5 Salmonid abundance summary, total number of fish

and percent, Elwha estuary

East

estuary

West

estuary

Impounded

estuary

Combined

estuary

Total salmon

Number 250 2,527 2 2,780

Percent 9 91 0 100

Chinook

Number 130 1,942 1 2,073

Percent 6 94 0 75

Coho

Number 37 335 0 372

Percent 10 90 0 14

Chum

Number 37 180 0 217

Percent 17 83 0 10

Cutthroat

Number 2 65 0 67

Percent 3 97 0 2

Steelhead

Number 44 5 1 50

Percent 88 10 2 2

Table 6 Comparison of Shannon–Wiener ecological diversity

(H) values for the three areas of Elwha estuary, by month

Month Groups na F or t P

March 3 2/10/2 2.282 0.16

April 3 6/12/6 9.413 0.001

May 3 7/15/10 8.571 0.001

June 2 8/6 2.881 0.018

July 2 10/8 3.956 0.001

August 2 4/6 1.215 0.23

a n values are for East/West/Impounded areas respectively

Table 7 Percent similarity results, fish species and densities,

Elwha estuary

Comparison Percent

similarity

West vs. Impounded 39

East vs. West 61

East vs. Impounded 69

Fig. 2 Comparison of mean values for fish distribution indices

for the three areas of the Elwha Estuary, for the entire

migration season (left side) and by month (right side), 2007: (a)

diversity (H0), (b) species richness, and (c) density (fish/m3).

Error bars represent the 95% CI. a Impounded site sampled

during March–May

b

Hydrobiologia (2009) 636:179–190 185

123

side channel habitat and a reduction in suitable

eulachon spawning habitat (Shaffer et al., 2007).

Sediment delivery to the estuary is also extremely

variable and is documented to result in localized

rising of the river bed (Draut et al., 2007, 2008). This

aggradation appears to have driven habitat function

of the east estuary during the course of this study by

forming a sediment lens at the entrance to the east

estuary that prevented many fish from using the east

estuary.

When combined, the hydrologic disruptions of

sediment deposition and diking appear to be contrib-

uting to reduced ecological indices and salmon species

densities in a significant portion of the Elwha estuary

by preventing fish from accessing areas of the estuary.

The presence of fish in both the east and impounded

areas of the estuary, and high numbers of fish in the

impounded estuary indicates both areas are suitable

habit for fish, provided they can access the habitat. The

intermediate nature of indices and salmon densities in

the east estuary indicate that the barrier to fish

distribution to this part of the estuary is recent, and

given how it formed, likely to be temporary. The

significantly lower species richness, and dominance of

stickleback (a long-lived non-migratory species), and

lack of juvenile salmonids in the impounded estuary

indicates that, due to the permanent and total physical

access barrier for both river and marine fish, it is

functioning differently from the other sites, with lower

long-term ecological function for fish.

There may be factors other than the changes in

sediment deposition and connectivity, which could

have resulted in the observed differences in fish

distribution within the Elwha estuary. Differences in

observations of the east and west estuary may be

attributed to sampling effort. The west estuary is much

smaller than the east estuary. Fish in the east estuary

had a larger area to inhabit, and may have had a lower

probability of capture due to limited sampling area

relative to the habitat available. Trends in ecological

indices and fish abundance, however, do not support

this alternate explanation. Ecological indices and

salmon densities in the east estuary initially were

similar to those in the west estuary, and also increased

with the salmon migration periods. The trends then

drop off within the east estuary only, indicating a

Fig. 3 Mean density (fish/m3) of the five salmonid species and total salmonids, grouped by location within the Elwha Estuary,

March–August 2007. Error bars represent the 95% CI

186 Hydrobiologia (2009) 636:179–190

123

disruption to access to the east, but not west, estuary.

We therefore postulate that outmigrating juvenile

salmon used the east estuary when they could get to

it, that the blockage progressed during the outmigration,

and that the still-outmigrating salmon responded by

using the only estuarine habitat left available to them,

the small fragment of west estuary habitat. This is

further evidenced by the salmon size across the estuary.

Although it varied, overall, the similarity in size of

Chinook, coho, and chum sampled from the east and

west estuary suggests that fish of the same population

and year class were in the east and west estuary, and

grew across the outmigration season, but there were

significantly fewer of them in the east estuary, which

could be predicted if east estuary access was

prevented. Alternatively, fish distribution differences

might be a result of different habitat characteristics

between the east and west estuary. While this may be

the case between the long isolated impounded area

and the rest of the estuary, there is no evidence that

the overall estuarine habitat structure and features

are significantly different between the east and west

estuary. These two sides of the Elwha estuary have no

permanent disconnect from each other or the river, are

at the same tidal elevation, and have the same aspect

exposure to the shoreline and river. Finally, if the

observed fish distribution differences were due to

differences in estuarine habitats of the three areas, we

would have expected to see consistent differences in

fish and ecological metrics across the estuary instead of

a relative drop in fish abundance and ecological indices

mid-season, and concomitant shift in similarity from

east and west estuary to east and impounded estuary.

Alternatively, sediment processes may have

resulted in a blockage at the connection of the west

estuary to the main river, and the fish observed in the

west estuary were simply resampled through the

season, resulting in artificially inflated fish abundance

observations for the west estuary. While this would

also be a clear linkage between anthropogenic alter-

ation of physical process and habitat function, there are

several observations to counter this. Specifically, if the

fish numbers observed in the west estuary were a result

of resampling, we would have expected to see the same

Fig. 4 a Averaged fork length (mm) for salmonid species

observed in the East and West areas of the Elwha Estuary,

summarized for March–August 2007. b Salmonid species

length by month, observed in the East and West areas of the

Elwha Estuary, during March–August 2007. East Estu-

ary = circle, West Estuary = triangle. Error bars represent

the 95% CI

Hydrobiologia (2009) 636:179–190 187

123

trends in total fish numbers in the west and impounded

estuary. Instead, we saw very different trends in fish

numbers in the impounded and west sections of the

estuary, and somewhat different trends between the

east and west estuary. For example, chum abundances

increased steadily in the west estuary (but not in the

impounded or east portions of the estuary), indicating

that the west estuary had regular fish access while the

other areas of the estuary did not. Among the three

areas, the impounded estuary (for the months sampled)

and east estuary appeared to be similar—and in some

cases almost identical—for ecological indices and fish

distribution, indicating that the east estuary and

impounded estuary are similar in fish distribution

due to lack of fish access. The disruption to the east

estuary is presumed to be due to a sediment lens,

formed from well-documented and very disrupted

sediment delivery processes that block fish access.

Fig. 4 continued

188 Hydrobiologia (2009) 636:179–190

123

Because this lens was created by river hydrodynamics

in an extremely variable system, it is a temporary

habitat alteration. Ecological implications of tempo-

rary blockage are at this time unknown, but worthy of

further study. For example, these observations are

consistent with those of Harrison & Whitfield (1995),

who defined similar trends in fish distribution and

ecological linkages within an estuary that is regularly

occluded due to sedimentation. The disruption to the

impounded estuary, on the other hand, is due to the

dike, which is a permanent habitat feature. Ecological

implications of this permanent barrier are likely much

more severe than those associated with temporary

barriers, and a priority for further detailed study.

Our results illustrate the important relationship

between anthropogenic changes to a watershed, and

the role diking and disruption of physical processes of

sediment transport and hydrologic connectivity play in

estuarine habitat utilization by fish. We believe that

fish distribution observed in this study indicates (1)

Diking clearly changes fish distribution of an estuary;

(2) Sediment delivery can result in the same barrier to

fish as a diking; and (3) Juvenile salmonids can

respond fairly quickly to a dynamic sediment land-

scape. If our third conclusion is correct, providing the

fish with the most alternatives for estuarine habitat is

the best alternative for estuarine management and

salmon recovery. The most obvious opportunity for

providing more habitat is to provide hydrologically

restored fish access to the impounded west estuary.

This restoration should be conducted sooner than later.

While the current sediment processes of the Elwha

estuary are dynamic, they will be even more so with

the large sediment pulses that will affect the estuary

within 5 years of dam removal. Dramatic changes in

sediment transportation and river flow are expected

before that natural functionality of the river will be

recovered. During this period, sedimentation pro-

cesses, and associated habitat accessibility, in the

estuary will likely fluctuate. Ecosystem restoration to

allow full hydrologic restoration of the Elwha estuary

should, therefore, be initiated as soon as possible to

allow fish the maximum opportunity for estuarine

habitat access during dam removal and concurrent

habitat restoration.

Concurrent ecosystem monitoring should be initi-

ated as soon as possible, including detailed longer-

term monitoring of fish movement in the estuary as

well as more detailed long-term physical habitat

mapping, including sediment mapping of the river

and estuary to the river mouth, and water quality

monitoring of all elements of the Elwha estuary and

shoreline are a priority. Monitoring should include

defining components of the Elwha estuary prior to

dam removal. Specifically, channel area and type

(blind versus open) and vegetation type (riverine

tidal, scrub–shrub, and emergent marsh), and detailed

water quality should be quantified throughout the

estuary, prior to, during, and after dam removal.

These studies should be conducted concurrently with

long-term fish distribution assessment to quantify the

relationship we have identified in this study.

Acknowledgments This study was sponsored in part by the

North Olympic Peninsula Lead Entity, and by the Salmon

Recovery Funding Board (SRFB), United States

Environmental Protection Agency (EPA), the Washington

Department of Fish and Wildlife (WDFW), and the Lower

Elwha Klallam Tribe. The Clallam Marine Resources

Committee provided funding for two college interns. Student

interns were also provided by Peninsula College Fisheries

Program and Center of Excellence’s NSF REU program, and

Western Washington University. Mr. Jack Ganzhorn and Dr.

Dwight Barry provided student supervision. Nancy Bluestein-

Johnson provided student guidance. Interns who assisted in the

project include Jesse Charles, Chris DeSisto, Bryan Hara, Erica

Hirsh, Mario Laungayan, Romy Laungayan, Ross McDorman,

Sean Oden, Tiffany Nabors, Jacob Ray, Melanie Roed, Justin

Rondeau, Trista Simmons, Ben Warren, Karen Wilkie, Eric

Wood, and Steve Wyall. Jenna Schilke, formerly WDFW,

supervised a portion of the field work. Private property owners

Pam Lowry and Malcom Dudley along with Chuck Janda

provided site access. Project in kind partners in the order of

contribution included Cathy Lear (Clallam County), Dave

Parks (DNR), Brian Winter (ONP), Ross Fuller, Mike Sharpf,

Chris Byrnes, Roger Mosley, Dan Penttila, Dan Doty, and Tim

Quinn (WDFW), Bruce McCarter (DFO),Tim Randle (BoR),

and Amy Draut (USGS). Kurt Fresh (NOAA) and two

anonymous reviewers provided valuable critical manuscript

review. This material is based on research supported in part by

the National Science Foundation under REU Grant No.

0452328 awarded jointly to Peninsula College and Western

Washington University. Any opinions, findings and conclu-

sions, or recommendations expressed in this material are those

of the authors, and do not necessarily reflect the views of the

National Science Foundation.

References

Beamer, E., R. Henderson, A. McBride & K. W. Wolf, 2003.

The importance of non-natal pocket estuaries in Skagit

Bay to wild Chinook salmon: An emerging priority for

restoration. Skagit River System Cooperative, Research

Department, La Connor, Washington.

Hydrobiologia (2009) 636:179–190 189

123

Beamer, E., A. McBride, C. Greene, R. Henderson, G. Hood,

K. Wolf, K. Larsen, C. Rice & K. L. Fresh, 2005. Delta

and nearshore restoration for the recovery of wild Skagit

River Chinook salmon: linking estuary restoration to wild

Chinook salmon populations. Supplement to Skagit Chi-

nook Recovery Plan. Skagit River System Cooperative,

La Conner, Washington.

Draut, A. E., J. B. Logan, R. E. McCoy, J. A. Warrick, E. Todd,

M. McHenry & D. M. Rubin, 2007. Channel Evolution on

the Lower Elwha River 1939–2007. Proceedings, 2007

GSA Annual Meeting. Denver, Colorado.

Draut, A. E., J. B. Logan, R. E. McCoy, M. McHenry & J.

Warrick, 2008. Channel evolution on the lower Elwha

River, Washington, 1939–2006. USGS Scientific Investi-

gations Report 2008–5127. U.S. Geological Survey,

Menlo Park, CA.

Duda, J. J., J. E. Freilich & E. G. Schriener (eds), 2008. Dam

Removal and Ecosystem Restoration in the Elwha

Watershed. Northwest Science 82(Special Issue): 1–12.

Edgington, E. & P. Onghena, 2007. Randomization Tests, 4th

ed. Chapman & Hall/CRC Press, Boca Raton, FL.

Fresh, K. L., 2006. Juvenile Pacific Salmon in Puget Sound.

Puget Sound Nearshore Partnership Report No. 2006–06.

Seattle District, U.S. Army Corps of Engineers, Seattle,

Washington.

Gregory, R. S., 1993. The effect of turbidity on the predator

avoidance behavior of juvenile Chinook salmon (On-corhynchus tshawytscha). Canadian Journal of Fisheries

and Aquatic Sciences 50: 241–246.

Gregory, R. S. & C. D. Levings, 1998. Turbidity reduces

predation on migrating juvenile Pacific salmon. Transac-

tions of the American Fisheries Society 127: 275–285.

Harrison, T. D. & A. K. Whitfield, 1995. Fish community

structure in three temporarily open/closed estuaries on the

natal coast. Ichthyological Bulletin of the J. L. B. Smith

Institute of Ichthyology, Grahamstown, South Africa 64:

1–80.

Hood, W. G., 2002. Application of landscape allometry to

restoration of tidal channels. Restoration Ecology 10:

213–222.

Hood, W. G., 2004. Indirect environmental effects of dikes on

estuarine tidal channels: Thinking outside of the dike for

habitat restoration and monitoring. Estuaries 27: 273–282.

Hothorn, T., K. Hornik, M. A. van de Wiel & A. Zeileis, 2008.

Implementing a class of permutation tests: The coin

package. Journal of Statistical Software 28: 1–23.

Huo, M., P. Onghena & E. Edgington, 2006. RT4Win: Ran-

domization tests software for Windows, version 1.0.

Katholieke Universiteit Leuven, Belgium.

Marshall, S. & M. Elliott, 1998. Environmental influences on

the fish assemblage of the Humber estuary, UK. Estuarine,

Coastal and Shelf Science 46: 175–184.

McCune, B., J. Grace & D. Urban, 2002. Analysis of Eco-

logical Communities. MjM Software Design, Gleneden

Beach, OR.

Pess, G. R., M. L. McHenry, T. J. Beechie & J. Davies, 2008.

Biological impacts of the Elwha River dams and potential

salmonid responses to dam removal. Northwest Science

82(Special Issue): 72–90.

Pohl, M., 2004. Channel bed mobility downstream from the

Elwha dams, Washington. The Professional Geographer

56: 422–431.

R Development Core Team, 2008. R: A Language and Environ-

ment for Statistical Computing. R Foundation for Statistical

Computing, Vienna, Austria. http://www.R-project.org/.

Randle, T. J., J. Bountry, B. Jackson & G. Smillie, 2004. Elwha

River Restoration Draft Sediment Monitoring and Man-

agement Plan. U. S. Department of the Interior, Bureau of

Reclamation and National Park Service. Port Angeles,

Washington.

Shaffer, J. A., D. Penttila, M. McHenry & D. Vilella, 2007.

Observations of Eulachon, Thaleichthys pacificus, in the

Elwha River, Olympic Peninsula, Washington. Northwest

Science 81: 76–81.

Shaffer, J. A., P. Crain, B. Winter, M. McHenry, C. Lear & T.

Randle, 2008. Nearshore restoration of the Elwha River

through removal of the Elwha and Glines Canyon Dams:

An overview. Northwest Science 82(Special Issue): 48–59.

Todd, S., N. Fiztpatrick, A. Carter-Mortimer & C. Weller,

2006. Historical changes to estuaries, spits, and associated

tidal wetland habitats in the Hood Canal and Strait of Juan

de Fuca regions of Washington State. PNPTC Technical

Report 06 01. Point-No Point Treaty Council, Kingston,

Washington.

Toft, J. D., J. R. Cordell, C. A. Simenstad & L. A. Stamatiou,

2007. Fish distribution, abundance, and behavior along

city shoreline types in Puget Sound. North American

Journal of Fisheries Management 27: 465–480.

Warrick, J. A., G. R. Cochrane, Y. Sagy & G. Gelfenbaum, 2008.

Nearshore substrate and morphology offshore of the Elwha

River. Northwest Science 82(Special issue): 153–163.

Warrick, J. A., D. George, G. Gelfenbaum, P. Ruggiero, G.

Kaminsky & M. Beirne, 2009. Beach morphology and

change along the mixed grain-size delta of the Elwha

River, Washington. Geomorphology 111: 136–148.

Williams, P. B., M. Orr & N. J. Garrity, 2002. Hydraulic

geometry: A geomorphic design tool for tidal marsh

channel evolution in wetland restoration projects. Resto-

ration Ecology 10: 577–590.

Winter, B. D. & P. Crain, 2008. Making the case for ecosystem

restoration by dam removal in the Elwha River. Northwest

Science 82(Special issue): 13–29.

Zar, J. H., 1984. Biostatistical Analysis. Prentice-Hall, Engle-

wood Cliffs, NJ.

190 Hydrobiologia (2009) 636:179–190

123