Skykomish Draft Final Report - Wild Fish Conservancy

Skykomish River Braided Reach
Restoration Assessment
Fish Use Analysis
Draft Final Report
June 28, 2006
Suggested citation: Drucker, E.G. 2006. Skykomish River Braided Reach Restoration
Assessment: Fish Use Analysis. Draft Final Report, June 28, 2006, prepared by
Washington Trout for Snohomish County Surface Water Management, Everett, WA.

Introduction
Snohomish County Surface Water Management and partners have proposed to identify and
prioritize opportunities to restore reach-level channel processes within the braided section of the
Skykomish River extending from the cities of Gold Bar to Sultan, WA. The braided reach
(“study reach”) includes over ten miles of mainstem channel between “Big Eddy” in Gold Bar
(rm 43.3) and Sultan (rm 33), and nearly seven miles of interconnected side channels (Figs 1–7).
In 2004 Washington Trout (WT) surveyed the braided reach in support of the following project
goals:
• to describe patterns of current fish use within the study reach to define a baseline against
which future conditions can be compared;
• to identify critical fish habitats so that restoration actions with high likelihood of creating
and maintaining these habitats can be prioritized;
• to evaluate the biological cost and benefit of proposed restoration actions.
Washington Trout’s 2004 field work served two general tasks designed to evaluate fish use
within the braided reach. First, fish species composition and relative abundance were surveyed
seasonally within a subsample of habitat units chosen to represent the overall habitat-type
distribution in the study reach. The specific objectives of these surveys were (i) to compare
species diversity and relative density of adult and juvenile fishes in the study reach’s mainstem
and in associated side channel networks; (ii) to identify physical habitat features significantly
related to fish relative density, including habitat unit type and size, and within-unit survey
location (e.g. channel center versus edge habitat; unit middle versus upstream–downstream unit
interface; Fig. 8); and (iii) to examine seasonal and diel variation in species composition,
distribution, and relative abundance.
The second task related to fish-use assessment was characterization of salmon spawning activity
in the study reach. Redd and carcass surveys were performed in order to (i) quantify the
incidence and timing of spawning activity throughout the braided reach; (ii) to document
species-specific patterns in the spatial distribution of spawning; and (iii) to examine the
relationship between spawning activity and physical habitat characteristics.
Patterns of fish use in the Skykomish River braided reach provided guidance for developing both
a general strategy and specific projects for restoring and protecting habitat. Recommendations
for designing and prioritizing such projects are presented in Chapter X.
Methods
Reach Nomenclature
The braided reach was partitioned into distinct habitat units (pools, riffles, glides) according to
the Snohomish County Preliminary Habitat Analysis of July 2004 (Figs 1–7). To facilitate
comparison among units, unique identifier numbers were assigned to each mainstem and side
channel habitat unit surveyed. Side channel networks were named from upstream to downstream
as follows: SCA (right-bank channel near the city of Gold Bar) (Fig. 3), SCB (left-bank network
near Gold Bar) (Fig. 3), SCC (left-bank network between the cities of Startup and Sultan) (Figs
5, 7), SCD (right-bank network near Sultan) (Fig. 6).
Preliminary habitat-type designations, based on inspection of channel morphology in aerial
photographs taken during summer low-flow conditions, were ground-truthed by Washington
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Trout in August and September 2004. During these summer surveys, WT crews qualitatively
assessed each mapped unit’s physical characteristics including water depth, velocity, and surface
turbulence. These observations were measured against the geomorphic definitions of each unit
type following Cramer (2001):
Pool: a unit with residual depth and no surface turbulence except at its inflow.
Glide: a unit with no residual depth, little surface turbulence, and relatively uniform flow
velocity.
Riffle: a unit with discernable gradient and surface turbulence.
Several of the preliminary habitat type designations in the mainstem channel were modified on
the basis of WT’s on-site surveys. When correction of the original habitat unit type resulted in
two consecutive units of the same type, the two units were consolidated into a single larger unit
and renamed accordingly (e.g. mainstem unit “70+71”). In side channels, where most mapped
habitat units were pools, WT crews identified and named a number of additional units not
appearing on the preliminary maps. Note that the fish use surveys, which relied on these
corrected preliminary maps, preceded the final habitat unit delineation based on quantitative, onsite
physical surveys (cf. Appendix X). Fish survey areas and final habitat unit boundaries were
largely congruent; in cases where areal discrepancies were large, associated fish use data were
excluded from analysis.
Species Composition and Relative Abundance
Snorkel surveys were performed seasonally (Table 1) to provide estimates of fish species
diversity and relative abundance within the braided reach. Survey teams were comprised of
three snorkelers who floated abreast in a downstream direction during daylight hours (summer,
fall and winter 2004), and at night (winter 2004), recording in notebooks the species, life stage
(young-of-year and yearling juvenile versus adult) and number of all fishes observed within each
habitat unit. Waterproof habitat unit maps and aerial photographs (Figs 2–6) were used to assist
in identifying habitat unit boundaries in the field.
Surveyors occupied three longitudinal snorkel lanes, one located in the center of the channel and
one at each channel edge (Fig. 8) (cf. Fig. 3 in Pess et al., 2002; Cramer, 2001 p. 42). Snorkelers
changed lanes frequently between habitat units to minimize potential spatial bias in fish counts.
The width of each snorkel lane was defined by visibility on the day of the survey. Although
adult fish could be discerned underwater at distances up to 25 feet in the summer and up to 15
feet in the fall (Table 1), the maximum distance at which the smallest juvenile fish could be
confidently identified was approximately 5 feet (cf. Hillman and Chapman, 1989). Each snorkel
lane, therefore, was conservatively estimated as 10 feet wide. Within each habitat unit polygon
(Figs 2–6) the ten-foot wide curvilinear corridor along the unit’s longitudinal midline was used
to calculate snorkel lane area. To approximate relative fish densities for each habitat unit, total
fish counts were divided by the estimated total wetted area surveyed (i.e. three-times snorkel
lane area). As emphasized previously (Cramer, 2001), fish relative density calculated from a
large-river census of this type must be considered representative only of the surveyed fraction of
the total habitat area.
To examine patterns of within-unit spatial variation in the relative density of fish species
observed, each mainstem habitat unit was partitioned into nine survey subareas. The three
longitudinal snorkel lanes defined left-bank, center, and right-bank areas; units were further
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partitioned into upper, middle and lower thirds (Fig. 8). The latter divisions were approximated
in the field by consulting aerial photographs. The area of channel edge habitat surveyed within a
unit (A E ) was taken as the sum of the left-bank and right-bank subareas. Habitat unit interface
area (A I ) was calculated as the lower one-third of a given unit’s survey area plus the upper onethird
of the adjacent downstream unit’s survey area. Relative densities (count m -2 ) then were
calculated for (i) upper, middle and lower survey areas within units by dividing corresponding
fish counts by one-third of the total unit survey area; (ii) edge habitat areas within units by
dividing the sum of left- and right-bank fish counts by A E (i.e. two-thirds of the total unit survey
area); and (iii) habitat unit interface areas using fish counts within A I . This sampling approach
allowed testing of the hypothesis that relative fish density in habitat unit subareas with relatively
great physical heterogeneity (channel edge and habitat unit interface) exceeds that in more
homogeneous habitats (channel center and middle) (cf. Fig. 8).
For both mainstem and side channel survey areas, fish densities were calculated individually for
juveniles and adults of each species observed, and for five species categories: (1) all fish species;
(2) all salmonids (juvenile and adults); (3) adult salmonids; (4) juvenile salmonids; and (5) ESAlisted
salmonids (Chinook salmon and bull trout, adults and juveniles). For salmonid categories
2–4, mountain whitefish (Prosopium williamsoni) were excluded on the basis of the species’
relatively high abundance and unthreatened status (Snohomish River Basin Salmon Recovery
Forum, 2005).
After an initial reconnaissance snorkel of the mainstem in late July 2004, a baseline of fish use
data for summer 2004 was obtained over the course of five days (early August to early
September) by snorkeling every mapped mainstem habitat unit between rm 34.5 and rm 43.3
(units 1–74 consecutively; Figs 2–6) as well as the majority of mapped units within side channel
networks SCB (22 units) and SCC (30 units) (Tables 1, 3). In the subsequent fall 2004 survey,
mainstem habitat units were sampled by a stratified (proportional allocation) subsampling
protocol (EPA, 2002). Specifically, habitat units of different types were selected randomly for
survey in proportion to the frequency of their occurrence within two contiguous segments of the
study reach with distinct geomorphological profiles (cf. Appendix X): “Big Eddy” in Gold Bar to
Startup and Startup to the mouth of the Sultan River (Table 2). The mainstem was subsampled
using this protocol on a single day in fall 2004 (mid November). Selected units in side channel
network SCC were surveyed in winter 2004 (late December) to allow seasonal comparisons with
summer fish use data from this network. Preliminary observations on diel variation in fish
distribution and relative abundance were also made during this winter survey (cf. Table 1). WT
crews attempted to snorkel side channel network SCD and the adjacent mainstem reach (i.e.
below the mouth of the Sultan River; Skykomish rm 33–34.5) in December 2004 but extremely
poor visibility in both areas precluded the collection of fish use data. Snorkel sites and habitat
unit sample sizes for all 2004 side channel surveys are listed in Table 3.
Spawning Surveys
Washington Trout coordinated with Washington Department of Fish and Wildlife personnel to
identify the range of dates that typically encompasses the spawning runs of Chinook, chum and
coho salmon in the Skykomish River braided reach. On four days within this range during fall
2004 (between September and December; Table 1), WT field crews conducted surveys
throughout the mainstem channel and side channel networks SCA, SCB, SCC and SCD (rm 33–
43.3) to record evidence of salmon spawning activity. Surveys were performed by boat and on
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foot; polarized sunglasses were worn to facilitate observation of salmon redds and carcasses. At
each redd, the following data were collected:
• redd location (using GPS);
• redd habitat (pool, riffle, glide, tailout, channel edge/bank);
• redd substrate (cobble, gravel, sand);
• presence (and number) or absence of live spawners.
When reduced water visibility precluded identification of the species of fish on a redd, or when a
redd was unoccupied, WT crews made presumptive species assignments based on observed
physical characteristics of the redd. The “chinook (assumed)” assignment was given to isolated
redds exceeding 4 feet in length and occurring in large-cobble mainstem habitat; “chum
(assumed)” was assigned to clustered redds, each less than 4 feet in length, occurring in side
channel habitat units.
From each salmon carcass observed, the following data were collected:
• carcass location (using GPS);
• species;
• sex;
• body length;
• presence/absence of adipose fin;
• spawning status (when practical, body cavities of female fish were opened to inspect the
degree of egg retention).
Statistical Analyses
To facilitate comparison with other fish use studies, average relative fish densities in the
Skykomish River were calculated from fish counts and survey areas of all habitat units surveyed,
regardless of fish presence or absence. For the purpose of statistical analysis, however, adjusted
relative densities were calculated following Pess et al. (2002). In the Skykomish braided reach,
as in other large river systems of the northwest thus far studied, many fish species and age
classes are absent from the majority of habitat units sampled by snorkelers (G. Pess, NOAA
Fisheries, Northwest Fisheries Science Center, pers. comm.). As a result, relative abundance
data are commonly dominated by zero counts; such data skew greatly reduces the power to
detect statistically significant differences in density when fish are present. Except where noted
otherwise (e.g. Table 4), this study reports adjusted relative fish density, defined as the fish count
per square meter of survey area excluding habitat units in which no fish were observed. These
‘where present’ density estimates are presented graphically together with data on the proportion
of surveyed habitat units with fish present (cf. Pess et al., 2002). Note that fish densities are
reported only for summer 2004, since habitat unit areas were not measured in other seasons
during which snorkel surveys were performed. In this report, fall and winter 2004 relative
abundance data appear as absolute counts.
The assumptions of parametric statistical methodology were evaluated by conducting K-S
normality tests and Bartlett’s tests for homogeneity of variance (StatView, SAS Institute Inc.).
When appropriate, one-way analysis of variance (ANOVA) was performed for each life stage of
each species to test whether adjusted relative density varies significantly with river system
(mainstem versus side channel and among side channel systems), habitat unit type (pool, riffle,
glide), within-unit survey area, and habitat-unit interface type (latter two factors evaluated only
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in mainstem). Scheffe’s tests were used for post-hoc comparisons. These analyses were
conducted on summer 2004 mainstem fish densities within three reaches: (1) entire study reach
(mainstem habitat units 1–74); (2) mainstem above the Startup levee (units 1–42); (3) mainstem
below the Startup levee (units 43–74) (see Figs 2–6). Units 42–43 spanning the levee were
selected as marking the approximate transition from higher gradient and faster flows to lower
gradient and slower flows in the mainstem (cf. Appendix X). Univariate ANOVA was used to
test for seasonal variation in relative abundance within the mainstem (summer versus fall 2004)
and within side channel network SCC (summer versus winter 2004). This method of analysis
was also applied to day versus night snorkel-survey data from side channel network SCC to
assess the significance of diel variation in fish counts. When assumptions of parametric testing
were not met, Kruskal-Wallis tests were used to investigate significant effects of spatial,
temporal and habitat-related variation on relative fish abundance and density.
Results
Habitat Designations
Preliminary habitat unit maps used during the 2004 fish use surveys are shown in Figures 1–7.
Adjustments to these maps made in the field (cf. Reach Nomenclature section of Methods) were
restricted to the mainstem channel; no changes in habitat unit type were recorded in the side
channel networks. Modifications of preliminary unit type in the mainstem are not presented
graphically here (see final habitat unit maps in Appendix X), but are reflected in the total count
of pools, riffles and glides surveyed (Table 2). Typical mainstem habitat surveyed is illustrated
in Figure 9.
The four side channel networks within the study reach differ markedly in size and complexity.
SCA (Fig. 3) is a single, broad channel connecting mainstem habitat units 12 (rm X) and 19 (rm
X). Network SCB (Fig. 3) extends downstream from mainstem unit 15 (rm X) via a well-defined
and continuously wetted channel (SCB) which rejoins the mainstem at unit 22 (rm X). Channel
SCB also contributes to an intermittently wetted channel (SCB1) which rejoins the mainstem
downstream at unit 30 (rm X). Network SCC (Figs 5, 7), the most complex within the
Skykomish braided reach, contains two distinct systems: a series of channels whose flow
originates from surface and possibly also subsurface discharge from the mainstem (channels
SCC, SCC1, SCC2, SCC3) and an apparent spring brook system with flow fed by groundwater
discharge (channels SBA, SBA1, SBA2, SBA3, SBA4). Collectively, this side channel network
connects mainstem habitat units 49 and 58D (rm X and Y, respectively). Network SCD (Fig. 6)
is comprised of a main channel extending from the mainstem pool immediately downstream of
unit 74 (rm X) to the downstream terminus of the study reach, and associated side channels
SCD1–SCD5. Representative habitats surveyed within the side channel networks are illustrated
in Figure 9.
Species/Age-Class Composition and Relative Abundance
Reach-Level Patterns
Washington Trout field crews made over 38,000 individual fish observations within the
Skykomish River study reach during snorkel surveys in 2004. Over the course of summer, fall
and winter surveys, ten species were documented in the mainstem channel and side channel
networks, of which seven were salmonids: bull trout, Salvelinus confluentus; Chinook salmon,
Oncorhynchus tshawytscha; chum salmon, Oncorhynchus keta; coho salmon, Oncorhynchus
kisutch; coastal cutthroat trout, Oncorhynchus clarki clarki; rainbow trout/steelhead,
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Oncorhynchus mykiss; and mountain whitefish, Prosopium williamsoni. Also observed were
largescale sucker, Catostomus macrocheilus; threespine stickleback, Gasterosteus aculeatus; and
sculpin, Cottus sp. The relative abundance of salmonids varied among habitat units from
roughly one-quarter to nearly 100% of the total fish count. In the mainstem and side channels,
snorkel survey area represented 19±10% and 26±21% (mean±S.D.), respectively, of total habitat
unit wetted area (Fig. 10).
Over 8,500 fish belonging to eight species were observed in the braided reach mainstem, with
mountain whitefish and largescale sucker among the most abundant during summer and fall
surveys (Fig. 11; Tables 5, 6). Adults of these two species were observed in a large proportion
of all mainstem habitat units surveyed (83% and 43%, respectively, during the summer) (Fig.
12C). Anadromous salmonids were dominated by coho, Chinook and chum salmon, and resident
salmonids were represented in greatest numbers by juvenile trout (Fig. 11). Fishes found only in
the mainstem during the intensive summer snorkel surveys (i.e. not also observed within side
channel networks) were juvenile and adult bull trout, and adult Chinook, steelhead, and
largescale sucker (Fig. 12).
Approximately 30,000 fish belonging to ten species were observed in the braided reach side
channel networks, with juvenile coho salmon far outnumbering all other fishes in the majority of
channels during summer and winter surveys (Fig. 13; Tables 7–10). In side channel networks
SCB and SCC, juvenile coho were documented in 69% of all habitat units surveyed during the
summer (Fig. 12A). Other salmonids observed in side channels, in order of decreasing relative
abundance, were rainbow and cutthroat trout, mountain whitefish, and juvenile Chinook salmon
(Fig. 13). Adult stickleback were observed at high relative densities but were patchily
distributed in the side channels, occurring in just 5% of habitat units surveyed; this species was
found only in the side channels (i.e. not also observed in the mainstem) (Fig. 12C).
Reach-level analysis of the summer 2004 snorkel-survey data revealed distinct patterns of spatial
variation in fish relative density. For several species and life stages, adjusted relative density
(i.e. density evaluated in habitat units with fish present) was significantly higher in the side
channel networks than in the mainstem channel. This pattern was found for juvenile Chinook
and juvenile coho salmon, adult rainbow trout, and juvenile rainbow/cutthroat trout (Fig. 12A,B).
A similar pattern was found for all species-summary categories examined. Although fish were
present in approximately 90% of all habitat units surveyed in both the mainstem and side
channels, the adjusted relative densities of all species observed, all salmonids, and ESA-listed
salmonids were significantly higher in the off-channel networks (Fig. 14).
Species diversity, age-class composition and relative abundance also varied between and within
the side channel networks. The two major networks, SCB and SCC, contained the same seven
fish species during summer snorkel surveys, but Oncorhynchus and Prosopium were represented
only by juveniles in SCB while SCC held both juvenile and adult trout and whitefish (Tables 7–
9). In addition, SCB during the summer contained significantly higher densities of juvenile
largescale sucker (t-test: d.f.=6; P

flow system also contained significantly more fish (i.e. higher average count of all fish species
within pools) during the summer than either the spring brook or mainstem (t-tests: d.f.=23, 32;
P

and overall was comprised of three fewer species of salmonids than the summer population
(Tables 5, 6). Chum salmon succeeded Chinook as the most prevalent adult anadromous fish
(Fig. 11A,B). In addition, the ratio of juvenile-to-adult trout and salmon observed in pools fell
from approximately 10 to 0.01 over this period, reflecting a pronounced change in life historystage
usage of the mainstem during the day.
Snorkel survey data collected during summer and winter 2004 in side channel network SCC
highlights additional seasonal variation in fish relative abundance, diversity, and age class
structure. Mean daytime fish counts in surface-flow and spring-brook side channel pools
showed a significant decrease between the two survey seasons, a pattern also observed in
mainstem pools between summer and fall (Fig. 22A). The daytime winter population in side
channel network SCC lacked five species observed in the summer (rainbow and cutthroat trout,
sculpin, largescale sucker and mountain whitefish) but contained adult chum salmon (Table 10).
As in the mainstem, a seasonal reduction in the relative abundance of juvenile salmonids was
measured in side channel network SCC. Between summer and winter, the ratio of juvenile-toadult
trout and salmon observed in pools during daylight hours fell roughly 2000-fold in the
surface-flow side channel system, and 20-fold in the spring brook channels. Associated with
these patterns of seasonal variation in fish use was an 8–13 °C average decline in daytime water
temperature in mainstem and side channel pools (Fig. 22B).
Paired day–night snorkel surveys were performed in side channel network SCC in December
2004 to test the hypothesis that fish are in fact present within side channel pools during the
winter, but take cover during daylight hours. These surveys revealed that both juvenile and adult
trout and salmon, presumably seeking refuge during the day, indeed emerge during the night.
Both surface-flow and spring-brook side channel pools showed a trend toward increasing overall
relative fish abundance (i.e. juveniles and adults of all species) at night; this pattern was
statistically significant for pools fed by surface flow (t-test: d.f.=14; P

Chinook and chum were 14% (1 of 7 carcasses examined) and 16% (10 of 63 carcasses),
respectively. The single female coho carcass found in the braided reach was also a PSM
candidate, bearing full and intact egg skeins.
The locations of all salmon redds and carcasses observed during the spawning surveys are shown
in Figs 2–7. The general pattern evident from these maps is that the distribution of salmon
spawning activity is species-specific. Chinook redds were built primarily in the mainstem, often
near the channel bank (e.g. units #7–13 [Fig. 2] and unit #45 [Fig. 4]), while chum redds were
most commonly found within the four side channel networks (Figs 3, 5, 6, 7, 24A). Several
exceptions to this pattern of non-overlapping spawning areas are noted: Chinook and chum redds
were found together within mainstem units #18–20 at the mouth of side channel network SCA
(Fig. 3). The only instance of confirmed chum redds outside the immediate vicinity of a side
channel was in mainstem unit #35 (Fig. 3). Chinook and chum carcasses showed a similar
distribution to that of redds (Fig. 24B). Although largely restricted to distinct spawning areas,
carcasses of the two species were found in proximity within side channel SCB, resembling the
adjacent mainstem in its habitat unit diversity (Fig. 3), as well as in a seasonal backwater channel
in the vicinity of mainstem units #42–44 (Fig. 4) and in the lower reaches of side channel SCC
(Figs 5, 7). A large proportion of chum redds were occupied by live spawners (93% of mainstem
redds and 86% of side channel redds), whereas Chinook redds contained live fish less frequently
(22% in mainstem; 57% in side channels) (Fig. 24A).
The habitat preferences of spawning salmon in the braided reach were examined in detail by
analyzing the physical characteristics of redd sites. The majority of Chinook redds were
observed in glides, while a large proportion of chum redds were built in pools; for both species,
riffle habitats were also frequently selected for spawning (Fig. 25A,B). Chinook redds were
constructed almost exclusively in large cobble; chum salmon utilized a variety of substrates,
including cobble, gravel and sand (Fig. 25C,D). The depth of water in which redds were
constructed did not differ significantly between Chinook (mean 13.4 in.) and chum (mean 16.4
in.) (t-test: d.f.=116; P=0.09).
Washington Trout’s spawning surveys were generally more extensive in their geographic
coverage than were snorkel surveys within a given channel system. Accordingly, the spawning
surveys provided information about fish use that helped refine the distributional data obtained
from snorkel surveys earlier in the year. For example, the small left-bank braid of the mainstem
at habitat units #38–39 was dry during summer 2004 and excluded from snorkel surveys. In
November, the same channel was found to contain the highest density of chum salmon redds
within the braided reach (Fig. 4).
Sources of Sampling Bias
Discussion
Fish Abundance and Density
Fish counts obtained by snorkel survey typically underestimate the “true” number of fish present
in a habitat unit as determined by more accurate methods of measuring fish abundance (e.g.
electrofishing/removal, mark–recapture) (Rodgers et al., 1992). The calibration recommended
by Hankin and Reeves (1988) involving adjustment of snorkel counts by the ratio of “true” fish
numbers to snorkel estimates was not performed in this study because exhaustive removal
methods were not feasible in the large habitat units surveyed (see also Thompson and Lee, 2000;
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Burnett, 2001). Accordingly, the Skykomish River snorkel counts are assumed to be negatively
biased, but since the amount of bias is unknown they are used only to provide estimates of
relative abundance and density.
Snorkel-survey area represented an approximately constant proportion of total habitat unit
wetted area for small and intermediate-sized units in both the mainstem and side channels. For
the largest units sampled (>25,000 m 2 in the mainstem and >7,000 m 2 in the side channels),
however, survey area comprised a disproportionately small fraction of total unit area (Fig. 10).
Hence, fish densities recorded for these largest units may be artificially low due to sampling
bias. The inverse relationship between Oncorhynchus mykiss density and habitat unit area (Fig.
16) suggests preferential use of smaller units by juvenile and adult trout, but it is important to
recognize that true densities in the largest units may be higher than those observed.
Water velocities in the Skykomish mainstem prevented snorkelers from surveying in an
upstream direction, as is typical in studies of smaller river systems (e.g. Hankin and Reeves,
1988) to avoid disturbing or displacing fish. This study, therefore, was subject to potential
observer bias in fish distribution within habitat units. However, a consistent pattern of declining
relative abundance from upstream to downstream within units, an expected result of such bias,
was not observed.
Variation in water clarity during summer and fall snorkel surveys must also be taken into
consideration when interpreting the relative fish abundance patterns described here. The marked
seasonal decline in fish counts within the mainstem and side channels (Figs 21, 22) is likely due
in part to reduced daytime visibility during surveys performed later in the year (Table 1).
Patterns of Fish Density in the Skykomish and Other Northwest Rivers
Comparison of fish abundance data among river systems is complicated by variation in
enumeration methodology used in different studies (Lister and Genoe, 1970; Rodgers et al.,
1992). Such comparison is further confounded by sampling performed at different times of year
and by the use of different means for calculating relative fish density. To facilitate accurate
comparison of relative density data from the Skykomish River braided reach and from other
large northwest river systems we examine below densities derived from snorkel surveys of the
same season and consider different density metrics separately.
The traditional index of mean relative fish density, widely reported in fish use studies, is the
average number of individuals observed per unit area in all habitat units surveyed, including
those units with fish absent. For juvenile salmon and trout in the Skykomish braided reach, this
traditional density measure falls within the ranges reported for other northwest river systems.
Specifically, the average relative densities of juvenile trout and Chinook salmon measured
during summer in the Skykomish mainstem (Table 4) match those documented in other large
river mainstems (i.e. >50 m bankfull width), including the Wenatchee (WA) and Grande Ronde
(OR) (Table 15) (see also review by Bartz et al., 2006).
An alternative mean density index, which excludes from consideration all surveyed habitat units
with fish absent, can be employed when fish are patchily distributed among units to facilitate
parametric statistical analyses (cf. Methods). This adjusted relative fish density, or “where
present” density index, is not currently in widespread use but here is compared among sites for
which data are available. The mean adjusted relative densities of adult Chinook salmon,
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steelhead and whitefish measured in the Skykomish River mainstem during summer snorkel
surveys (Fig. 12A–C) are very similar to those reported by Pess et al. (2002) for the North Fork
Stillaguamish River (WA). In addition, juvenile salmon and trout exhibited mean summer
“where present” densities in the Skykomish mainstem (Fig. 12A,B) that closely match those
recorded for the mainstem Elwha River (WA) (Pess et al., 2002). In off-channel habitat, mean
adjusted relative densities of juvenile salmonids from the Skykomish and Elwha in summer
show general agreement with the exception of juvenile Chinook, for which average summer
“where present” densities were an order of magnitude higher in the Skykomish side channel
networks (cf. Fig. 12A, Table 15).
Patterns of spatial and temporal variation in fish density in the Skykomish braided reach are also
largely consistent with those documented in other large northwest rivers. The relatively great
abundance of juvenile coho salmon in side channel network SCC during summer (Fig. 13B,C)
reflects the well-documented importance of off-channel floodplain habitat for coho rearing (e.g.
Nickelson et al., 1992). Juvenile coho counts in side channel network SCC exceeding those in
side channel network SCB and in the Skykomish mainstem (Figs 11A, 13) may be related to
site-specific variation in water temperature. Mean summer temperatures measured in pools were
up to 8 °C cooler in side channel network SCC than in network SCB or the mainstem, reflecting
the possible use by juvenile coho of groundwater-influenced off-channel habitat in network SCC
as thermal refugia (cf. Brown, 2002).
The marked decline in relative fish abundance between summer and fall/winter measured in the
Skykomish during daylight hours (Fig. 22A) is likely related to the reduced swimming
performance of fish at low temperatures. As reviewed by Brown (2002), juvenile salmonids
may migrate to protected sites, including the interstices of river bed substrate, to avoid predation
and to reduce energy expenditure when swimming ability is compromised. The diel variation in
fish counts recorded in December 2004 within Skykomish side channel network SCC (Fig. 23)
matches a general behavioral pattern documented for salmonids during winter: residing in cover
during the day and emerging to feed at night (Lister and Genoe, 1970; Hillman et al., 1989;
Peters et al., 1998; Brown, 2002).
The hypothesis that habitats with relatively great physical heterogeneity support higher densities
of fish than more homogeneous habitats received partial support from this study. In the
Skykomish mainstem, juvenile salmonids exhibited significantly higher relative densities at the
edges of habitat units, especially those with marginal woody debris and riprap, than in the center
of units (Fig. 18D, Table 11). A similar pattern has been noted for juvenile salmonids in other
Pacific Northwest rivers (e.g. Lister and Genoe, 1970; Cramer, 2001; Jeanes and Hilgert, 2001;
Brown, 2002; Beamer et al., 2005). The concentration of adult fish in the less physically
complex centers of habitat units (Fig. 18A–C) may be a function of the relative scarcity of large
woody debris in the Skykomish mainstem and of the ability of adults to navigate more
effectively the higher water velocities of the thalweg. Despite the presumed physical
heterogeneity of habitat unit interfaces (cf. Fig. 8), neither juvenile nor adult fish showed their
highest relative densities in these areas, typically aggregating more densely in the adjacent,
longitudinal “middles” of units (Fig. 19). It is notable, however, that salmonids were more
frequently observed in these transitional habitats, raising the possibility that unit interfaces
support relatively low-density, evenly distributed populations rather than function as discrete
distributional “hot spots.” Further study of transitional habitats in the Skykomish and other river
systems is warranted to improve our understanding of the relationship between fish use and
habitat complexity.
11

Patterns of Salmon Spawning Activity
Spawning surveys of the Skykomish braided reach performed independently by Washington
Trout and by Washington Department of Fish and Wildlife (WDFW) in fall 2004 allow a
valuable comparison of redd count data collected by different techniques. During the two weeks
for which data are available from both sources, redd counts obtained by boat and on foot (WT)
closely match those obtained by aerial survey (WDFW). Specifically, 118 Chinook redds were
counted by WDFW on September 26, 2004 between “Big Eddy” in Gold Bar, WA to the mouth
of the Sultan River; 85 Chinook redds were counted by WT four days later in the same reach. At
the end of the Chinook spawning run, WT and WDFW each recorded zero Chinook redds
(surveys on November 9 and November 10, 2004, respectively) (Table 12; Jackson, 2005b). The
total number of Chinook redds documented by WT in the Skykomish braided reach during fall
2004 (136), however, represents roughly one-third of the total tally reported by WDFW (418)
(Jackson, 2005a). This discrepancy may reflect differences in total area surveyed, survey effort
(i.e. number of flights/surveys), error in salmon species-assignment of redds, and/or techniquespecific
variation in sensitivity of redd detection.
The Skykomish River 2004 redd survey data underscore the importance of the braided reach as a
productive salmon spawning ground. Of 840 Chinook redds documented by WDFW in fall 2004
between the mouth of the Skykomish River and the anadromous fish barrier at Sunset Falls (rm
51.5), approximately 50% were observed in the braided reach. The number of Chinook redds
observed per river mile in the braided reach (49.2) exceeded that in all other WDFW survey
reaches on the Skykomish River in 2004 (Table 13).
The documentation of pre-spawning mortality in female Chinook, chum and coho salmon within
the braided reach (see Results) adds to a growing set of PSM observations across western
Washington. To date, the phenomenon has been noted for several salmonid species with
intensive spawning studies focused on both rural/residential habitats and urban creeks (e.g.
Glasgow et al., 2005; McMillan et al., 2006; N. Scholz, NOAA Fisheries, Northwest Fisheries
Science Center, pers. comm.). Ongoing work by Washington Trout and by NOAA Fisheries
seeks to refine understanding of the current geographic extent of PSM in the Pacific Northwest
and to identify causal factors, including patterns of land use and water quality, related to PSM
incidence.
12

Summary
Fish species composition and relative abundance:
• During summer, fall and winter 2004 snorkel surveys of the Skykomish River braided
reach, ten fish species were documented in the mainstem channel and side channel
networks, of which seven were salmonids and two were ESA-listed (bull trout and
Chinook salmon).
• Relative fish densities measured by snorkel survey during summer in the Skykomish
braided reach were generally similar to those recorded for other large northwest rivers.
• Relative fish density was generally higher in the side channel networks than in the
mainstem channel during summer. This pattern was significant for all ESA-listed
salmonids encountered. Side channel pools supported relatively more fish than mainstem
pools during winter.
• Juvenile coho salmon far outnumbered all other fishes in the majority of side channels
surveyed during summer and winter 2004, occurring in nearly 70% of all habitat units
examined.
• Fish species diversity, age-class composition and relative abundance varied significantly
between and within the Skykomish River side channel networks.
• The adjusted relative density (i.e. density measured only for habitat units with fish
present) of adult and juvenile rainbow trout/steelhead exhibited an inverse relationship
with habitat unit wetted area during summer.
• Significantly higher densities of adult trout and salmon were observed in mainstem pools
than in mainstem riffles or glides during summer. Juvenile salmonids in the mainstem
were found in highest densities within riffles during summer, but in the side channel
networks, no significant relationship between fish density and habitat unit type was
detected.
• Summer fish densities measured in the Skykomish mainstem exhibited distinct patterns
of within- and between-unit spatial variation: (a) adult salmonids were typically found in
higher densities within the center of habitat units than at unit edges, while juvenile
salmonids aggregated more densely in edge habitat including large woody debris and
riprap bank armoring; (b) adult and juvenile salmonids were more frequently observed in
the transition area between habitat units than in the longitudinal “middle” of units, but
within these interfaces fish densities were relatively low. Pool-riffle and riffle-pool
transitions contained significantly higher salmonid densities, on average, than all other
habitat unit transitions studied.
• Mean daytime fish counts in both the mainstem and side channels declined sharply
between summer and fall/winter. During winter, mean counts increased at night for most
fish species and age classes examined.
13

Summary, continued
Salmon spawning activity:
• During fall 2004 spawning surveys of the Skykomish braided reach, the majority of
salmon carcasses encountered were female Chinook and chum of presumed natural origin
(intact adipose fins). Pre-spawning mortality (i.e. death prior to egg deposition) was
documented in 14% of Chinook females and 16% of chum females.
• The distribution of salmon spawning activity was species-specific: Chinook redds were
built primarily in the mainstem, often near the channel bank, while chum redds were most
commonly found within side channels.
• Redd counts obtained by boat survey and on foot approximated those obtained by
WDFW aerial surveys in fall 2004. Both datasets highlight the Skykomish River braided
reach as an important salmon spawning ground.
14

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Wenatchee, WA, pp. 43-82. Don Chapman Consultants, Inc., Boise, ID.
15

Jackson, C. (2005a). Email to E. Drucker reporting unpublished WDFW redd count data,
December 5, 2005.
Jackson, C. (2005b). Email to E. Drucker reporting unpublished WDFW redd count data, June
22, 2005.
Jeanes, E. D. and Hilgert, P. J. (2001). Juvenile salmonid use of lateral stream habitats, Middle
Green River, Washington, 2000 Data Report. Prepared by R2 Resource Consultants, Inc.
July 19, 2001, Redmond, WA, viii+63 pp. & appendix.
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history of naturally produced spring Chinook salmon in the Grande Ronde River basin.
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16

Rodgers, J. D., Solazzi, M. F., Johnson, S. L. and Buckman, M. A. (1992). Comparison of three
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17

Figure Legends for maps on pages 19–25
Fig. 1. Overview of the Skykomish River braided reach with preliminary habitat type
designations. Contiguous segments of the study reach are illustrated in greater detail in Figures
2–7. Note that final habitat type designations are presented in Appendix X.
Fig. 2–6. Preliminary habitat type designations and observed salmon spawning activity within
the Skykomish River braided reach. Redd and carcass data were collected between September
and December 2004 (Tables 1, 12).
Fig. 7. Detailed view of side channel network SCC (cf. Fig. 5).
18

Figure 8. Schematic illustration of the snorkel-survey subareas within each mainstem habitat
unit. Two consecutive units are depicted. Ten-foot wide snorkel lanes (gray shading) defined
left, center, and right subareas. Upper, middle and lower subareas of equal size were defined by
transverse boundaries (approximated in the field). The area of edge habitat surveyed within each
unit was taken as the sum of left and right subareas. Habitat unit interface area was taken as the
sum of adjacent lower and upper subareas in consecutive units.
26

Figure 9
Representative Skykomish River braided reach habitats surveyed in 2004
Snorkel survey of mainstem habitat unit #48 on left-bank
(November 2004).
Snorkel survey of isolated pool in lower reach of
side channel SCB1 (August 2004).
Snorkel survey of pool within side channel network SCC (December 2004).
27

Figure 9 (continued)
Representative Skykomish River braided reach habitats surveyed in 2004
Upstream view of confluence of side channel SCC (at left)
and SBA1 (October 2004).
Chum redd with live fish (in background) within
side channel SCC (October 2004).
Spawning survey of side channel SCD (December 2004).
28

Figure 10. Relationship between snorkel-survey area and total habitat unit wetted area in Skykomish
River braided reach during summer 2004. Linear regression lines are shown for small to intermediate
sized habitat units in the mainstem (y=0.150x+323.0; r 2 =0.66) and in the side channels
(y=0.133x+63.3; r 2 =0.87). In the largest units, survey area comprised a disproportionately small
fraction of total unit area. Side channel data are pooled values from networks SCB and SCC.
29

Figure 11. Fish species composition and relative abundance in mainstem Skykomish River
braided reach assessed by seasonal snorkel surveys. Pie charts present counts of largescale
sucker, mountain whitefish and ‘other’ fishes (sculpin and unidentified non-salmonid juveniles)
for all pools, riffles and glides surveyed. Bar charts illustrate relative abundance of all salmonids
excluding whitefish; juveniles and adults of these species are totaled separately (shown above
and below dashed lines, respectively). Counts of largescale sucker and mountain whitefish are
the sum of juvenile and adult counts for each species. Fish count totals: 8,206 in summer 2004
(76 units surveyed); 326 in fall 2004 (20 units). All counts made during daylight hours.
30

Figure 12 (legend on p. 33)
31

Figure 13 (legend on p. 33)
32

Figure 12. Relative densities of all fish species and age classes observed in the Skykomish River
braided reach during summer 2004 snorkel surveys. The adjusted (“where present”) density of
each species/age class is shown together with the proportion of surveyed habitat units with fish
present. All data presented as mean±S.E.M.; densities calculated from an average of 14 habitat
units per species/age class (range: 1–60 units). Significant differences in relative density
between the mainstem (MS) and side channels (SC) (pooled data from networks SCB and SCC)
were assessed by univariate ANOVA: *, P

Figure 14. Relative fish densities for five species categories (defined in text) from summer 2004
snorkel surveys of the Skykomish River braided reach. The adjusted (“where present”) density
of each category is shown together with the proportion of surveyed habitat units with fish
present. All data presented as mean±S.E.M.; densities calculated from an average of 46 habitat
units per category (range: 29–67 units). Significant differences in relative density between the
mainstem and side channels (pooled data from networks SCB and SCC) were assessed by
univariate ANOVA: *, P

Figure 15. Comparison of adjusted relative densities of (A) juvenile coho salmon and (B)
juvenile largescale sucker in pools within side channel networks SCB and SCC during summer
2004. Data are presented as mean±S.E.M. with number of pools sampled. Asterisks indicate
significant differences in relative density at P

Figure 16. Relationship between adjusted relative fish density and habitat unit area for trout and
steelhead in the Skykomish mainstem and side channels (pooled data from networks SCB and
SCC) during summer 2004.
36

Figure 17. Relative fish densities for different habitat unit types in the Skykomish braided reach
mainstem during summer 2004. Adjusted (“where present”) densities are presented for selected
species as mean±S.E.M. with associated proportions of units with fish present and number of
units sampled. Asterisks indicate significant differences in relative density at P

Figure 18. Relative fish densities for habitat unit edges and centers (cf. Fig. 8) in the Skykomish
braided reach mainstem during summer 2004. Adjusted (“where present”) densities are
presented for selected species as mean±S.E.M. with associated proportions of survey subareas
with fish present and number of subareas sampled. Asterisks indicate significant differences in
relative density at P

Figure 19 (legend on p. 40)
39

Figure 19. Relative fish densities for habitat unit middles and adjacent unit interfaces (cf. Fig. 8)
in the Skykomish braided reach mainstem during summer 2004. Adjusted (“where present”)
densities are presented for selected species as mean±S.E.M. with associated proportions of survey
subareas with fish present and number of subareas sampled. Asterisks indicate significant
differences in relative density at P

Figure 21. Seasonal variation in Skykomish mainstem fish counts (juveniles and adults of all
species; daytime surveys). Data are presented as means with S.E.M. errors bars and habitat unit
sample sizes. Mean fish counts in all unit types sampled declined significantly from summer to
fall (t-tests: d.f.=19, 40, 31; P

Figure 22. Spatial and seasonal variation in (A) daytime fish counts (juveniles and adults of all
species) and (B) corresponding daytime temperatures in Skykomish braided reach pools. Data
are presented as means with S.E.M. errors bars and pool sample sizes for the surface flow and
spring brook systems within side channel network SCC (summer and winter) and for the
mainstem (summer and fall) (cf. Table 1). Mean summer counts were significantly higher in the
surface-flow side channels than in either the spring brook side channels or the mainstem
(univariate ANOVA: P

Figure 23. Diel variation in winter fish counts (juveniles and adults of all species) for side
channel pools within the Skykomish braided reach. Data from December 2004 snorkel surveys
of side channel network SCC are presented as means with S.E.M. error bars and pool sample
sizes. Asterisk indicates significant difference in average daytime and nighttime fish counts
within surface-flow side channel pools (univariate ANOVA: P

Figure 24. Distribution of salmon redds and carcasses in the Skykomish braided reach. MS,
mainstem; SC, side channels.
44

Figure 25. Salmon redd counts by habitat unit type (A, B) and by substrate type (C, D). Redds
for which habitat and substrate determinations were not recorded during spawning surveys are
not enumerated here; see Table 12 for total redd counts.
45