POTENTIAL SALMONID PRODUCTION CAPACITY OF FRESHWATER HABITAT IN STREAMS TRAVERSING ACTIVE AGRICULTURAL LANDS OF SKAGIT COUNTY, WASHINGTON

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POTENTIAL SALMONID
PRODUCTION CAPACITY OF
FRESHWATER HABITAT IN
STREAMS TRAVERSING ACTIVE
AGRICULTURAL LANDS OF
SKAGIT COUNTY, WASHINGTON

Prepared for
Skagit County
Planning and Permit Center

March 2003

1400 Century Square
1501 4th Avenue
Seattle, Washington 98101
(206) 438-2700
TABLE OF CONTENTS

                                                                                                                                         Page
1.0        INTRODUCTION ..................................................................................................................1
2.0        METHODOLOGY .................................................................................................................2
           2.1  ANALYSIS OF SALMONID HABITAT TRAVERSING AGRICULTURAL
                LAND.......................................................................................................................2
           2.2  SMOLT DENSITIES .................................................................................................5
           2.3  POTENTIAL AVERAGE SMOLT PRODUCTION.....................................................7
           2.4  POTENTIAL AVERAGE ADULT RETURNS............................................................8
           2.5  POTENTIAL ESCAPEMENT AND EXPLOITATION NUMBERS.............................9
           2.6  POTENTIAL INCREASES IN PRODUCTION CAPACITY...................................... 10
3.0        RESULTS............................................................................................................................ 12
4.0        DISCUSSION ...................................................................................................................... 15
5.0        REFERENCES..................................................................................................................... 18

APPENDICES

APPENDIX A-TABLES
   Table 1. Salmonid Habitat in Skagit DEIS Study Area
   Table 2. Salmonid Parr and Smolt densities
   Table 3. Potential Salmonid Smolt Production
   Table 4. Potential Salmonid Adult Returns
   Table 5. Potential Salmonid Escapement and Exploitation Numbers

APPENDIX B-ECONOMIC ANALYSIS

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POTENTIAL SALMONID PRODUCTION CAPACITY OF FRESHWATER HABITAT IN

       STREAMS TRAVERSING ACTIVE AGRICULTURAL LANDS OF SKAGIT COUNTY

                                                     1.0         INTRODUCTION

The potential anadromous salmonid production capacity of freshwater habitat in streams traversing active
agricultural lands has been calculated for this report using the best available data and the best availa ble
methodologies in the literature. Production capacity has been calculated for species and stocks that occur
within streams that traverse agricultural lands. The species/stocks analyzed are fall/summer run chinook
salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch), chum salmon (O. keta ), pink salmon (O.
gorbuscha), winter run steelhead trout (O. mykiss mykiss), and sea-run coastal cutthroat trout (O. clarki
clarki). Although anadromous summer run steelhead, spring run chinook salmon, sockeye salmon (O.
nerka), and native char [bull trout (Salvelinus confluentus) and Dolly Varden (S. malma )] occur in Skagit
County, they spawn and rear as juveniles in headwater streams upstream from the study area and only occur
in study area stream segments as spawner or smolt migrants (or as foraging adult sea-run coastal cutthroat
and native char).

An assessment of the physical habitat area in stream segments traversing or bordering active agricultural
lands was made using available data. Average smolt production values in smolts/meter2 were applied to the
calculated habitat areas to determine the potential production of smolts in a completely functioning forested
landscape. Smolt production numbers were multiplied by the appropriate average marine survival rates for
each species and basin to determine potential adult returns. These returns include escapement (number of
naturally spawned fish returning to natal streams), and exploitation (commercial, tribal, and sports catch)
numbers. Expected escapement and exploitation numbers were calculated using available data on
escapements and catches during previous years.

The smolt production, adult returns, and escapement/exploitation numbers derived from the above
calculations represent the average potential of a completely functioning mature conifer and mixed
conifer/hardwood forest landscape, such as would occur in a National Park or Wilderness Area. A review of
the literature regarding the effects of land use and land cover on the functional characteristics of salmon
streams and their production potential indicated that average salmonid production values in a landscape
dominated by agriculture are approximately 30% of those in a completely functioning forested landscape
consisting of conifer and mixed conifer/hardw ood stands. Salmonid production values reported in the
literature for a rural-residential landscape averaged approximately 60% of a mature forested landscape.
Stream and riparian habitat functionality in a commercial forest were reported to be approximately halfway
between those of a rural-residential landscape and a forested landscape in a National Park. This would be
about 80% of a mature forested landscape.

To estimate the value of riparian buffers or active management of functional characteristics of stream and
riparian habitat, increases in production capacity from an agricultural baseline were estimated for restoring

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the functional characteristics of stream and riparian habitat dominated by agricultural land use to 100%
(landscape dominated by mature forest), 80% (landscape dominated by commercial forest), and 60%
(landscape dominated by rural and residential use) of its functional capacity.

An economic analysis of the economic impacts of increases in salmon productivity resulting from
implementation of a given Alternative is presented in Appendix B.

                                                     2.0        METHODOLOGY

2.1        ANALYSIS OF SALMONID HABITAT TRAVERSING AGRICULTURAL LAND

 A GIS coverage consisting of USGS National Landcover Data (1992) overlaid by hydrological data from the
Skagit County GIS Departme nt (2003), including incorporated Washington Department of Natural Resources
stream types and Salmon Steelhead Habitat Inventory Assessment Program (SSHIAP) anadromous fish
presence data in conjunction with StreamNet (2003) anadromous fish presence data was used to determine
the total length in meters of anadromous fish stream habitat that traverses agricultural land in Skagit County.
The 1992 USGS National Landcover Data was incorrectly referenced as USGS (2000) in chapter 3 of the
Skagit County CAO DEIS. This was recorded by individual stream (tributary or side channel/slough) in all
of the anadromous salmonid streams in Skagit County that traverse agricultural land. The mainstem habitat
of the Skagit River was not included because current land use activities in the Skagit River basin are more
likely to affect side channels than mainstem habitats (Beechie et al. 1994). Potential impacts on the main
stem occur largely as a result of flood control activities and existing federal and Washington State laws
provide for a greater level of environmental review and protection for projects within mainstem areas
(Beechie et al. 1994). Much of the mainstem floodplain habitat is diked or leveed, with agricultural activities
restricted to land on the upland side of the dikes and levees. Forested riparian buffers on the upland side of
dikes or levees are not likely to contribute to riparian and stream functions on the floodplain side, although
the buffers would provide habitat for terrestrial riparian species, such as forest songbirds. Most of the habitat
analyzed was tributary habitat, which provides relatively small amounts of winter rearing habitat in the Skagit
River basin relative to side-channel and side-channel slough habitats (Beechie et al. 1994).

Habitat da ta for waterways (streams) traversing agricultural land in Skagit County are recorded in Table A-1
of the Appendix A. Habitat in individual waterways was separated into segments based on having the same
WDNR water type, average summer wetted width (approximately), stream gradient (divided into three
categories: 0%-2%, 2%-4%, and greater than 4%), channel type, and fish species present. Channel types
were divided into 6 classifications [tidal sloughs or blind tidal channels with tidal influence (Edison Slough
and Fisher Slough), straight ditched channels (Big Ditch/Maddox Creek, or Carpenter/Hill Ditch), freshwater
sloughs or side channels with at least 90% of surface area consisting of pools, large tributary mainstems
(average summer wetted width > 6 meters), small tributaries or independent streams (average summer wetted
widths < 6 meters), and blind tidal channel/creeks (blind sloughs fed by headwater creek/s)]. Segments were
not necessarily continuous, but consisted of the total lengths of each segment that traversed agricultural land.
For example, a series of GIS stream segments of a small tributary channel containing rearing habitat for coho
salmon, steelhead trout, and coastal cutthroat trout, with 0%-2% stream gradient, WDNR water type 3,

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average summer wetted width of 3 meters would be considered a single segment if GIS coverage (and
literature reports) indicate that summer wetted width is larger in downstream GIS segments and upstream
GIS segments only contain coastal cutthroat trout. The example segment could consist of 3 GIS segments (or
line arcs) with the same attributes that are 300, 400, and 900 meters long (for a total of 1,600 meters of
length). Following the example segment upstream, it could traverse or border agricultural land for 150
meters in one area, 230 meters in a second area, and 70 meters in a third and final area for a total of 450
meters of stream in the 1,600 meter segment that actually is in contact with agricultural land. For the purpose
of habitat calculations within the study area, the stream segment would be recorded as 450 meters in length
(the length of the segment that actually traverses or borders agricultural land).

Because GIS analysis of agricultural land for the CAO DEIS utilized GIS coverage of agricultural landcover
in the USGS National landcover data (USGS 1992), rather than Skagit County GIS coverage of Rural
Resource Natural Resource Lands (RRc-NRL) and Agricultural Natural Resource Lands (Ag-NRL), the
USGS National landcover data was used for the purpose of analyzing stream habitat and potential salmonid
production in this report. Because of this, many streams and stream segments that do not occur on lands
zoned for Rural Resource and Agricultural use were included in the report analysis, effectively increasing the
size of the study area to all lands utilized for Agricultural in Skagit County at the time of the last update of the
USGS National landcover data (1992). This data represents the best available land cover information
available at the time of the preparation of this report.

A length of stream was considered to traverse agricultural land if at least one bank of the stream was utilized
for agricultural purposes.        USGS landcover classifications considered agricultural land are
Orchards/vineyards/other, grasslands/herbaceous, pasture/hay, row crops, and small grains.                  The
grasslands/herbaceous classification would also apply to mountain meadows and utility right-of-ways.
Because the data was analyzed manually, rather than by query, it was possible to exc lude stream segments
traversing mountain meadows and utility right-of-ways. Chum and pink salmon outmigrate to salt water
soon after emergence as fry from spawning gravel, so only usable spawning gravel habitat in reaches utilized
by pink or chum salmon were measured for these species. GIS coverage from SSHIAP and StreamNet was
utilized to determine which stream segments were utilized by spawning chum and pink salmon.

Physical stream survey data available in the literature was incorporated wherever possible in determining
summer wetted widths, channel types, and stream gradients [Phillips et al. (1980), Johnson (1984, 1985,
1986), and Zillges (1977)]. Where literature data was not available, measurements were taken from aerial
photos and GIS data or stream width observations made by URS Biologists during field surveys. Stream
width data was not available for some streams that were too small to estimate stream widths from photos or
GIS coverage. Stream length (length of main stream channel) was given in miles (Williams et al. 1975).
This length was not used in calculations of habitat (pool, and riffle) areas. Segment length (the number of
meters of stream in a segment that traverse agricultural land) was used to calculate habitat areas (see
discussion below). A total of 43 stream basins above locations with known summer wetted stream widths
were measured for basin area in square miles using the Maptech Terrain Navigator application and
topographic data (Maptech 1999). Stream widths primarily came from Phillips et al. (1980), Johnson (1984,

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1985, 1986), and Zillges (1977). The paired stream width and basin area data were analyzed using the linear
regression function of the Microsoft Excel 2000 application. Data from 43 locations with a range of stream
width from 1 to 30 meters and basin area from 0.6 to 68.1 square miles were used. The regression analysis
yielded a formula of y=0.394801401431x + 2.40731325 with x=basin areas in miles2 and y=stream wetted
width at low flow in meters. The R-squared value was 0.91498116 and Correlation Coefficient was
0.956546475. The basin area for streams with no available width data were measured with the Maptech
application and the results used in the above regression equation to estimate approximate stream widths.

If data was available for the percent of pool and riffle habitat or percent of spawning gravel (Phillips et al.
1980), it was entered into the database and Table A-1 of Appendix A. The presence or absence of all
anadromous salmonids was also entered for each stream segment in Table A-1 of Appendix A. Dolly Varden
and bull trout presence was combined under “Char,” because the two species are difficult to distinguish
between and usually documented as “native char” unless genetic data is available (WDFW 1998). Bull trout
were not described as a species until 1978 (Cavender 1978) and native char documented before the early
1980s were recorded as Dolly Varden.

Segment lengths in meters were multiplied by summer wetted widths in meters to get segment areas in
meters2 . In most cases, pool and riffle percentages or percent gravel information was not available.
Estimates by stream gradient of pool and riffle percentages and the percent gravel by pool or riffle habitat for
western Washington streams in Table 16 of WDFW (2000) were used along with average pool and riffle
habitat percent in the Skagit River basin by stream gradient in Table 3 of Beechie et al. (1994) to develop
pool/riffle habitat percentages for streams by three stream gradient classifications (0-2, 2-4, and greater than
4%). The WDFW required interpolation because it was by 0-1, 1-3, and 3-5% gradients. The resulting
percentages are presented below in Table 1.

Table 1. Estimates of pool and riffle percentages and percent gravel estimates for western Washington.
      Stream                                                    Estimated %          Estimated % Pool     Estimated %
    Gradient (%)              Estimated % Pool                      Riffle                Gravel          Riffle Gravel
        0-2                          64                              36                     26                  40
        2-4                          50                              50                     35                  53
        >4                           34                              66                     34                  48

Pool and Riffle areas were estimated for each stream segment by multiplying segment area in meters 2 by the
percent pool and riffle habitat for the available literature data (Phillips et al. 1980) or stream gradient. Pool
and riffle areas were multiplied by percent pool gravel to obtain the areas of pool and riffle gravel in square
meters. Gravel data from Phillips et al. (1980) was not distinguished by habitat type and on gravel (total) area
in square meters was estimated for each segment using this data. Salmonids generally can only utilize
approximately 30% of available spawning gravels because of uneven distribution of spawning gravels, depth
and velocity requirements, and territorial behavior between spawning pairs (Bjornn and Reiser 1991). Usable
spawning gravel was calculated by multiplying the total gravel area for each stream segment by 0.30 (30%).

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2.2        SMOLT DENSITIES

Average smolt rearing densities in No./m2 of stream habitat for stream rearing species (ocean type chinook
salmon, coho salmon, and steelhead trout) were derived from the available literature. Smolt densities are
recorded in Table A-2 of Appendix A. There was no smolt density information available for sea-run coastal
cutthroat trout and average smolt densities were derived from rearing parr (age 1+ juveniles) density data in
Phillips et al. (1980).

In the case of pink salmon and chum salmon, which migrate as fry outmigrants soon after emerging from the
spawning gravel, smolt densities represent the expected average number of emergent fry per square meter of
usable gravel. Coho salmon smolt densities calculated in a similar fashion, based on available spawning
gravel and egg to smolt survival rates, was calculated for available usable spawning gravel in Big Indian and
No Name Sloughs, where it was suspected that smolt production may be spawning habitat, rather than rearing
habitat limited.

2.2.1      Coho Salmon

Rearing densities for coho salmon were calculated based on those densities used by Beechie et al. (1994) to
calculate smolt production in the Skagit River basin. These production figures were applied to all coho
salmon bearing streams in the study area. Separate densities were used for calculating summer and winter
rearing habitat densities in the three kinds of habitat found on agricultural lands (outside of the Skagit River
main channel). Potential average smolt densities used are presented below in table 2.

Table 2. Potential Average Smolt Density in Coho Smolts per meter2 (Slough and Tributary Habitat)
         or Distance in Kilometers (Main Channels of Tributaries over 6 meters in Summer Wetted
         Width).
                                                                             Tributary
          Slough                                           Pool                             Riffle
   Summer       Winter                        Summer                 Winter          Summer        Winter   Mainstem
    0.319        0.775                         0.425                 1.085            0.170        0.000     600/km

In addition to average smolt densities for rearing habitat, potential average smolt densities, based on available
spawning gravel and egg to smolt survival rates, was calculated for available usable spawning gravel in Big
Indian and No Name Sloughs, where it was suspected that smolt production may be spawning habitat, rather
than rearing habitat limited. Due to territorial behavior between spawning pairs, salmonids usually require an
area of spawning gravel per pair of four times the average redd area (Bjornn and Reiser 1991). The
recommended average area per spawning pair of coho salmon is 11.7 meters 2 (Bjornn and Reiser 1991). The
average number of eggs per spawning coho salmon female is 2,500 eggs (Beechie et al. 1994) for a total of
213.7 eggs per meter 2 of usable spawning gravel. The average egg-smolt survival from three literature
sources is 1.92% for an average coho smolt production of 4.1 smolts per meter2 of usable spawning gravel

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(Johnson and Cooper 1995, Bocking 2000, Bocking and Gaboury 2001).

2.2.2      Steelhead Trout

Two sets of densities were used to for steelhead trout. Phillips et al. (1981) averaged steelhead smolt
densities reporte d from 5 northwest watersheds (Keogh River, B.C.; Big Qualicum River, B.C.; Carnation
Creek, B.C.; Snow Creek, Washington; and Salmon Creek, Washington to get an average of 0.018 smolts per
meter 2 of stream habitat (regardless of habitat type). This smolt density was used by Phillips et al. (1981) to
calculate potential smolt production from the Skagit River basin and was used for one of the two sets of
steelhead smolt densities used in this report. Phillips et al. (1981) also reported that “excess” presmolt
juveniles from tributaries to the Skagit River are used in seeding mainstem rearing areas in the Skagit River
basin. And that, while 80% of the spawning in the basin occurred in tributaries, only 10% of the steelhead
smolting 2 years later were actually reared in the tributaries. Based on a spawning distribution of 80%
tributary and 20% mainstem, it was proposed that smolt production would be 0.14 smolts per meter2 in
tributary streams < 6 meters in summer wetted width and 0.0022 smolts per meter2 in mainstem habitat > 6
meters in summer wetted width. This second set of smolt densities was used for a second estimate of
potential steelhead smolt production.

2.2.3      Chinook Salmon

Smolt densities for the Skagit River basin of 1.78 per meter2 of slough habitat, 0.97 per meter 2 of stream
habitat with natural banks, 0.44 per meter 2 of stream habitat with gently sloping banks (bar habitat), and 0.348
per meter 2 of stream habitat with hydromodified banks were proposed in Hayman et al. (1996). The 1.78/m2
smolt density was applied in this report to all pool type habitat in side channel sloughs. Since information on
the slope of banks was not available, a conservative smolt density of 0.97/ m2 was applied to all stream
habitat containing rearing ocean type chinook salmon that was not hydromodified. Stream habitat with
hydromodified banks documented in Johnson (1986) as channelized or ditched received a smolt density of
0.348/ m2 .

2.2.4      Chum Salmon

With the exception that egg to fry survival, rather than egg to smolt survival, were used, the number of
emergent outmigrant chum salmon fry/smolts per meter of usable spawning gravel was calculated by
methodology similar to that used to calculate coho smolt production in Big Indian and No Name Sloughs.
The recommended average area per spawning pair of chum salmon is 9.2 meters 2 (Bjornn and Reiser 1991).
The average number of eggs per spawning chum salmon female is 2,870 eggs (Salo 1991), for a total of 312.0
eggs per meter 2 of usable spawning gravel. The average egg-fry survival for three northwest streams
referenced in Salo (1991) was 10.4% for an average chum salmon fry/smolt outmigrant production of 32.4
fry/smolts per meter2 of usable spawning gravel.

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2.2.5      Pink Salmon

The number of emergent outmigrant pink salmon fry/smolts per meter of usable spawning gravel was
calculated by methodology similar to that used to calculate chum smolt production. The recommended
average area per spawning pair of pink salmon is 2.4 meters2 (Bjornn and Reiser 1991). The average number
of eggs per spawning pink salmon female is 1,550 eggs (Heard 1991), for a total of 645.8 eggs per meter2 of
usable spawning gravel. The average egg-fry survival for seven northwest streams referenced in Heard
(1991) was 10.8% for an average pink salmon fry/smolt outmigrant production of 69.8 fry/smolts per meter2
of usable spawning gravel.

2.2.6      Sea-run Coastal Cutthroat Trout

There are no reported smolt densities in the literature for sea-run cutthroat trout. However, Phillips et al.
(1980) reported numerous densities for age 1+ juveniles (parr) rearing in Skagit River Tributaries. The
average density of parr cutthroat trout in Skagit River Tributaries was 0.052 per meter 2 (Phillips et al. 1980).
This figure was used for parr densities when none were reported in Phillips et al. (1980). The average age of
sea-run cutthroat smolts in Puget Sound reported in Johnson et al. (1999) is 2 years. Smolt densities were
calculated from average parr densities using average parr to smolt survival rate for steelhead trout of 28%
(Johnson and Cooper 1995).

2.3        POTENTIAL AVERAGE SM OLT PRODUCTION

Average smolt production is recorded in Table A-3 of Appendix A. Smolt production was calculated by
multiplying available habitat area by smolt densities. Density calculations were for each species were only
run for stream segments where the presence or rearing and spawning fish was documented by SSHIAP or
StreamNet data.

2.3.1      Coho Salmon

Coho salmon production was calculated for both winter and summer rearing habitat by multiplying the
appropriate smolt density by total kilometers of stream segment for tributaries over 6 meters in summer
wetted width, tributary pool or riffle area in square meters, and slough area in square meters. In the case of
Big Indian and No Name Sloughs, in addition to potential smolt production for rearing habitat, spawning
production capacity for smolts was calculated by multiplying the total area of usable spawning gravel by
number of smolts per square meter of usable spawning gravel.

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2.3.2      Steelhead Trout

Two methods were used to calc ulate steelhead smolt production. The first method multiplied stream segment
area in square meters by a smolt density of 0.018 smolts per meter 2. The second method multiplied stream
segment area for streams with a summer wetted width > 6 meters by a smolt density of 0.14 smolts per meter2
and segment area for streams with a summer wetted width < 6 meters by a smolt density of 0.0022 smolts per
meter 2.

2.3.3      Chinook Salmon

Chinook salmon smolt production was calculated by multiplying the segment area by a smolt density of 1.78/
meter 2 for pool habitat in sloughs, a 0.97/ meter2 smolt density for unhydromodified stream habitat, and a
0.348/ meter2 smolt density for documented (Johnson 1986) hydromodified stream habitat.

2.3.4      Chum Salmon

Chum salmon smolt production was calculated by multiplying a fry/smolt density of 32.4/ meter2 by the area
of usable spawning gravel in square meters for all stream segments with documented chum salmon spawning.

2.3.5      Pink Salmon

Pink salmon smolt production was calculated by multiplying a fry/smolt density of 69.8/ meter2 by the area of
usable spawning gravel in square meters for all stream segments with documented pink salmon spawning.

2.3.6      Sea-run Coastal Cutthroat Trout

Where smolt densities could not be calculated by data from Phillips et al. (1980), coastal cutthroat smolt
production was calculated by multiplying stream segment area in square meters by a smolt density of 0.052
smolts per meter2 . Smolt density values in meter2 calculated from parr densities from Phillips et al. (1980)
were used where this data was available for stream segments.

2.4        POTENTIAL AVERAGE ADULT RETURNS

Average potential adult returns are recorded in Table A-4 of Appendix A. Adult returns were calculated from
average marine survival values in the literature. Wherever possible, local marine survival values were used.
Marine survival represents the smolt to returning adult spawner percent survival. Adult returns include both
escapement (adult spawners returning to their spawning beds) and exploitation (commercial and sport caught
fish in the marine and stream environment). Percent marine survival was multiplied by smolt production to
calculate adult returns.

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2.4.1      Coho Salmon

A marine survival value of 11 percent for Skagit River basin coho salmon and 10 percent for Samish River
and independent drainages was used to calculate adult returns (Seiler et al. 2002).

2.4.2      Steelhead Trout

An average marine survival value of 9.1 percent was used for steelhead in the study area based on the average
values of northwest steelhead marine survival in the available literature (Johnson 1988, Johnson and Cooper
1991, Leland and Hisata 2001, Lirette et al. 1987, Blocking and English 1992, Bocking and Gaboury 2001,
Bocking 2000).

2.4.3      Chinook Salmon

An average marine survival of 2.6 percent was used based on average values reported in Beamer et al. (2000)
for the Skagit River basin.

2.4.4      Chum Salmon

An average marine survival of 2.0 percent was used based on reported marine survival rates for chum salmon
in the literature (Salo 1991, Leland and Hisata 2001).

2.4.5      Pink Salmon

An average marine survival rate of 2.9 percent was used based on reported marine survival rates for pink
salmon in the literature (Heard 1991).

2.4.6      Sea-run Coastal Cutthroat Trout

Marine survival rates for sea-run cutthroat trout are reported to be about 40% higher than those for steelhead
(Trotter 1997). Based on an average steelhead marine survival rate of 9.1 percent, a marine survival rate of
approximately 12.7 percent was used for sea-run coastal cutthroat trout.

2.5        POTENTIAL ESCAPEMENT AND EXPLOITATION NUMBERS

Potential escapement and exploitation numbers were calculated from SASSI data (WDFW and WWTIT
1994, SaSI 2001) and Washington (1994) for adult escapement and total adult return numbers. The average
percentage of escapement and exploitation in adult returns in presented below in Table 3. Because no data
was available for the Samish River, Skagit River chinook percentages were applied to Samish River chinook.
In the same fashion, information for independent drainages was not available for Chum, so the Samish River
percentages was applied to the nearby independent drainage of Colony Creek.

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Table 3. Potential Estimated Salmonid Escapement and Exploitation Numbers.
   Salmonid Stock                                                                    Exploitation (%)   Escapement (%)
   Skagit River Coho Salmon (1967-1982)                                                    68.6              31.4
   Skagit River Steelhead Trout (1977-1991)                                                15.4              84.6
   Skagit River Ocean Type Chinook Salmon (1974-1991)                                      40.4              59.6
   Skagit River Chum Salmon (1968-1991)                                                    72.0              28.0
   Skagit River Pink Salmon (1967-1991)                                                    51.8              48.2
   Samish River Coho Salmon (1967-1991)                                                    66.6              33.4
   Samish River Steelhead Trout (1987-1990)                                                11.4              88.6
   Samish River Ocean Type Chinook Salmon (1974-1991)                                      40.4              59.6
   Samish River Chum Salmon (1982-1991)                                                    46.1              53.9
   Independent Drainage Coho Salmon (1967-1991)                                            17.5              82.5
   Independent Drainage Chum Salmon (1982-1991)                                            46.1              53.9
In most cases, management restrictions on commercial and sports catches since 1991 have reduced the
exploitation rate on study area salmonids, decreasing the percent of the adult return that is captured by the
commercial and sports fisheries. Exploitation and escapement rates can normally be expected to vary over
time, with changes in management policy and the protection of special status species or stocks (such as Puget
Sound Chinook Salmon) by the Endangered Species Act.

2.6        POTENTIAL INCREASES IN PRODUCTION CAPACITY

As stated in the introduction, the average smolt production and adult returns calculated above were for fully
seeded stream habitat in a landscape dominated by mature coniferous or mixed conifer/hardwood forest
typical of a National Park or Wilderness Area. Beechie et al. (2003) analyzed riparian areas within the Skagit
River Basin by land cover type and estimated the approximate percentages of fully functioning forested
riparian habitat based on the presence of forested buffers at least 40 meters (131 feet) wide because they were
considered to provide more than 80% of wood recruitment and shading function as well as all of the root
strength and litter fall functions of stream riparian areas. Buffers under 20 meters (56 feet) wide were
considered impaired because they are likely to only achieve 50% of the wood recruitment of a mature
coniferous forest and 50% to 90% of the other 3 functions mentioned above. The results of the analysis of
Riparian functions vs. land cover type in Beechie et al. (2003) is summarized below in Table 4.

Table 4. Percentage of Fully Functioning Riparian Area by Land Cover Type.
   Land Cover Type                                                           Percent of Riparian Area Fully Functioning
   Agricultural                                                                                  13
   Urban (High Density)                                                                          15
   Rural (Low Density)                                                                           36
   Commercial Forest                                                                             58
   National Park/Wilderness Area                                                                 76
   National Forest                                                                               80

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Agricultural lands have been largely cleared of forest and are maintained as open areas except where there is
a lower terrace that is difficult terrain and is not tillable or poorly riparian lowlands that are too wet to plow
and are neglected or used only for grazing (Berg et al 2003). Most of the trees in these riparian areas left to
grow along stream margins are deemed unmerchantable (Berg et al. 2003). In addition to having about the
same amount of fully functioning riparian area as agricultural land, urban areas are usually defined as having
lots sizes between 0.125 and 0.5 acres in size, have high road densities, and a high percentage of impervious
surface area. Rural-residential area usually consist of larger estates between 1 and 5 acres in size and have a
much lower percentage of impervious surface area and lower road density. Commercial forest is managed on
a relatively short (usually < 80 year) rotation and has a smaller percentage of trees large enough to provide
the functions of wood recruitment, shade, root strength and litter fall. Timber harvest is not allowed in
National Parks and wilderness areas and much of the National Forest land is currently managed as Old
Growth Reserve to produce large mature trees suitable for obligatory old growth wildlife species (species that
require old growth timber).

Recent literature on the effects of land cover and land use on the functional characteristics of salmon streams
and their production potential indicate that the average salmonid production values in a landscape dominated
by agriculture or a completely clear-cut (unforested) landscape is approximately 30% (the average for 2
reported values in Table 5 was 32.1%) of those in a complete functioning forested landscape. Similarly,
literature values indicate production values in a landscape dominated by rural-residential land use of slightly
over 60% (average for 2 reported values of 64.8%) of those in a completely functioning forested landscape
(Pess et al. 2003 and Bilby et al. 2000). Salmonid production values in Pess et al. (2003) and Bilby et al.
(2000) are based on escapements of adult coho spawners in tributaries within the Snoqualmie River basin.
Coho require suitable gravel and pool rearing habitat in tributary streams, where they rear for approximately a
year. The dependence of coho on quality spawning and rearing habitat make them an excellent indicator
species for estimating production capacity of streams which are susceptible to environmental disturbances
associated with riparian functions.

The effect of removing riparian forest cover on available spawning gravels can be even more dramatic than
impacts to pool surface area. House et al. (1991) documented the effects of restoring coho salmon stream
habitat on Elk Creek and the upper Nestucca River (western Oregon stream basins). Fires, floods, and forest
management practices, particularly the removal of woody debris from stream channels had contributed to the
formation of homogeneous stream reaches dominated by riffles with little spawning gravel present. Stream
structure was restored through the installation of stream rehabilitation structures. After restoration, the stream
area increased in Elk Creek (3 years after restoration) and the upper Nestucca River (4 years after restoration)
57% and 14% respectively, pool volume increased approximately five- and twofold, water volume increased
over 60% for each stream, and gravel substrate increased 50- and 44-fold. Coho summer parr densities in Elk
Creek pools before and after rehabilitation were 0.93 fish/meter2 and 2.08 fish/meter 2. Coho summer parr
densities stream segments of the upper Nestucca River were 0.34 fish/meter 2 in untreated control sites and
0.82 fish/meter2 in rehabilitated sites.

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Table 5. Percent Salmonid Production in Relation to Land Cover Type.
   Dominate              Percent Salmonid Production in Relation to Land Cover Dominated
   Land                                           by Mature Forest
   Cover                         Pess et al. 2003                   Bilby et al. 2000             Average
   Rural                               68.2                               61.5                     64.8
   Agricultural                        30.3                               33.9                     32.1

Although Bilby et al. (2000) found spawning densities of coho salmon in lands dominated by rural and
agricultural land cover to be approximately 2 and 3 times less than those of forest dominated index reaches,
index reaches in regions dominated by urban (high density) land cover had coho spawning densities 13 times
less than forest dominated reaches or one fourth the spawning density of index reaches on land dominated by
agricultural use.

Beechie et al. (2003) analyzed functioning riparian areas within the Skagit River Basin and estimated that
within the Skagit River basin, riparian habitat along anadromous streams traversing commercial forest had a
functionality about half-way between that of riparian habitat within National Park/ Wilderness area and
riparian habitat in regions dominated by rural-residential land cover. Hence, I have applied a value of 80% to
commercial forest lands (half-way between that of rural land use and mature forest). I have applied the above
values of 100% of calculated smolt production and adult return for Mature Forest, 80% for Commercial
Forest, 60% for Rural-Residential land use, and 30% for agricultural land use. These salmonid production
percentages represent the effects of decreasing buffer widths.

The values of riparian buffers in Tables A-3, A-4, and A-5 of Appendix A were estimated projecting the
estimated increase in production capacity from an agricultural baseline of 30% of the full production capacity
of 100%, to 60%, 80%, and 100% of full production capacity by subtracting the values for 30% of capacity
from 60%, 80%, and 100% of full production capacity.

                                                           3.0          RESULTS

Results are given as summaries at the bottom of the pages in Tables A-3 (potential smolt production), A-4
(potential adult returns), and A-5 (potential escapement and exploitation numbers) of Appendix A. A
comparison of the smolt production capacity for coho salmon winter and rearing habitat indicates that it is
summer habitat limiting for coho salmon. The steelhead model utilizing separate smolt densities for
mainstem and tributary habitats was significantly higher than the single smolt density model. Considering
the life history of steelhead in the Skagit River basin reported by Phillips et al (1981), this may be the more
likely model of potential production capacity for steelhead trout. Analysis of coho smolt production capacity
from spawning vs. rearing habitat indicates that coho populations in No Name and Big Indian Sloughs are
currently spawning habitat limited. Summer and winter rearing capacity at even 30% capacity is likely to be
fully seeded by natural production from available spawning habitat. The full utilization of potential rearing
habitat in these basins would likely require the creation of additional spawning areas on tributaries draining
upland terrace or the continue planting of hatchery coho smolts.

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Average potential salmonid adult returns (assuming all stream segments occur in land cover dominated by
mature forest and have 100% functional stream and riparian habitat) are presented below in Table 6.

Table 6. Potential Salmonid Adult Returns for 51 Miles of Stream Length (100% Functional Stream
         and Riparian Habitat in Mature Forest).
                             Coho    Steelhead    Chinook       Chum       Pink      Cutthroat
 BASIN                      Salmon     Trout       Salmon       Salmon    Salmon       Trout
 Skagit River basin          6,570      620         3,733       12,683    28,166         803
 Samish River basin          2,306      153          399         3,645       –           100
 Colony Creek basin           258        –            –           395        –            20
 Edison Slough                 –         –            –            –         –            16
 No Name Slough*           423 (57)      –            –            –         –            25
 Big Indian Slough* 1,187 (141)          –            –            –         –            70
 Total Adult Returns         9,332      773         4,132       16,723    28,166        1,034
* Coho adult production calculated from available usable gravel. This number will be the number
   included in total adult returns.
Average potential salmonid adult returns for existing habitat (assuming stream and riparian habitat traversing
agricultural lands has approximately 30% the salmonid production capacity of salmonid habitat in mature
forest) are presented below in Table 7.

Table 7. Potential Salmonid Adult Returns for 51 Miles of Stream Length (30% Functional Stream
         and Riparian Habitat in Agricultural Land cover).
                            Coho      Steelhead    Chinook       Chum       Pink      Cutthroat
 BASIN                     Salmon       Trout       Salmon       Salmon    Salmon       Trout
 Skagit River basin         1,971        186         1,120        3,805     8,450        241
 Samish River basin          692          57          289         1,094                   30
 Colony Creek basin           77                                   118                    6
 Edison Slough                                                                            5
 No Name Slough*          127 (57)                                                        7
 Big Indian Slough*      356 (141)                                                        21
 Total Adult Returns        2,938        243         1,409        5,017     8,450        310
* Coho adult production calc ulated from available usable gravel. This number will be the number
  included in total adult returns.

The average potential increases in salmonid adult returns from an agricultural baseline that will occur if all
stream segments are restored to 100% functionality are presented below in Table 8.

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Table 8. Potential Increase in Salmonid Adult Returns from 51 Miles of Stream Length in
         Agricultural Baseline to 100% Functionality.
                                      Coho              Steelhead            Chinook   Chum
                                                                                     Cutthroat   Pink
 BASIN                               Salmon               Trout              Salmon    Salmon
                                                                                       Trout    Salmon
 Skagit River basin                   4,599                434                2,613     8,878
                                                                                        562     19,716
 Samish River basin                   1,615                133                 673      2,552
                                                                                         70
 Colony Creek basin                    181                                               276
                                                                                         14
 Edison Slough                                                                           11
 No Name Slough*           296 (57)                                                      17
 Big Indian Slough*       831 (141)                                                      49
 Total Adult Returns         6,593     567          3,286       11,706    19,716        723
* Coho adult production calculated from available usable gravel. This number will be the number
   included in total adult returns.

The average potential increases in salmonid adult returns from an agricultural baseline that will occur if all
stream segments are restored to 80% functionality are presented below in Table 9.

Table 9. Potential Increase in Salmonid Adult Returns from 51 Miles of Stream Length in Agricultural
              Baseline to 80% Functionality.

                                      Coho              Steelhead           Chinook    Chum      Pink    Cutthroat
   BASIN                             Salmon               Trout             Salmon     Salmon   Salmon    Trout
   Skagit River basin                 3,285                310               1,867      6,342   14,083     401
   Samish River basin                 1,153                 95                481       1,823               50
   Colony Creek basin                  129                                               197                10
   Edison Slough                                                                                             8
   No Name Slough*                   212 (57)                                                               12
   Big Indian Slough*               593 (141)                                                               35
   Total Adult Returns                4,765                  405               2,348   8,362    14,083     516

* Coho adult production calculated from available usable gravel. This number will be the number
  included in total adult returns.

The average potential increases in salmonid adult returns from an agricultural baseline that will occur if
all stream segments are restored to 60% functionality are presented below in Table 10.

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Table 10. Potential Increase in Salmonid Adult Returns from 51 Miles of Stream Length in Agricultural
Baseline to 60% Functionality.
                           Coho        Steelhead Chinook           Chum          Pink      Cutthroat
  BASIN                  Salmon          Trout        Salmon       Salmon     Salmon        Trout
  Skagit River basin       1,971          186          1,120        3,805       8,450        241
  Samish River basin        692            57           289         1,094                     30
  Colony Creek basin         77                                      118                       6
  Edison Slough                                                                                5
  No Name Slough*        127 (57)                                                              7
  Big Indian Slough*    356 (141)                                                             21
  Total Adult Returns      2,938          243          1,409        5,017       8,450        310
* Coho adult production calculated from available usable gravel. This number will be the number included in
   total adult returns.

                                                        4.0         DISCUSSION

The potential full (100%) production capacity estimated in this document is likely conservative (high)
because the calculations do not take into account conditions such as egg loss during redd construction and
egg retention in females. Pink salmon egg retention from 5 to 40 percent and egg losses over 50 percent have
been recorded in some streams (Heard 1991). Additional factors, such as excessive gravel scour, egg and fry
predation, and reduced intergravel flow during egg incubation and in-gravel residence of alevins are not
accounted for in the model. The models in this report also, do not consider interspecies competition (both
rearing juveniles and spawning adults) or competition with plants of hatchery smolts, again leading to a
conservative estimate of potential production of smolts and adult returns.

Many of the streams in the Skagit River basin experience rain-on-snow flow events, which can create high
fall and winter flows in channels normally dominated by peak flows created by spring snow melt. These
stream channels normally support primarily fall spawning species; such as coho, chinook, chum, and pink
salmon; rather than spring spawning species (steelhead and coastal cutthroat trout). During years with rain-
on-snow events in channels normally dominated by spring snow melt, egg to fry survival of fall spawning
salmonids is depressed due to gravel scour occurring below the depth of egg burial (Montgomery et al.
1999). As a result, estimates for salmonid smolt production for spring snow melt dominated streams where
rain-on-snow events frequently occur may be high.

For the range of flow-adjusted escapements of ocean type sub-yearling chinook since 1989, freshwater
rearing capacity does not appear to affect Skagit River smolt production (Beamer et al. 2000). Although at
some level of escapement, freshwater rearing capacity will likely limit production, there is no direct evidence
of what that population level is yet (Beamer et al. 2000). Chinook Salmon adult returns and smolt
outmigrants are directly correlated in the Skagit River system, indicating that freshwater rearing area is not a
limiting factor for chinook salmon at current levels of production. As a result, at current levels of
escapement, the potential smolt production and adult returns listed for chinook salmon in this report are

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probably greatly overestimated.

Responses of anadromous salmonids to habitat modification (rehabilitation, riparian buffers, etc.) are difficult
to measure (Reeves et al. 1991). Results often lack a basinwide context to accurately assess the effectiveness
of habitat modifications. Spawning and rearing fish may concentrate activities in recently modified habitats
within a basin without an actual increase in total numbers or an increase in the number or survival of
developing eggs and alevins or parr. It may appear that numbers have increased, when in reality there was
simply a redistribution of fish within a system (Reeves et al. 1991). The contribution of a stock or popula tion
to commercial and sport fisheries can be difficult to assess. An extended evaluation period is necessary to
assess the effects of habitat modification because of the tremendous natural variability in anadromous fish
populations (Hall and Knight 1981). There may be large natural fluctuations in site-specific density of
juveniles due to density-independent or density-dependent factors (Hall and Knight 1981). As in the
migration of steelhead fry in the Skagit River basin tributaries to mainstem rearing habitat (Phillips et al
1981), extensive movements from a basin of young salmonids that are not true smolts can occur.

It is unlikely that any riparian buffer or actively managed habitat alternative will result in 100 percent stream
and riparian habitat functionality. A more likely scenario would be an eventual increase in functionality to
between 60 and 80 percent of full habitat function as riparian buffers become mature forest or a managed
stream and riparian habitat achieves a higher level of function, enabling it to maintain anadromous salmonid
populations at higher levels that an agricultural land cover baseline.

As stated in section 2.6 (Potential Increases in Production Capacity), even using the assumptions from
Beechie et al. 2003, forested portions of buffers less than 56 feet in width, as in Alternative 2 of the Skagit
County CAO DEIS, may only achieve 50% of the wood recruitment of a mature coniferous forest and 50% to
90% of the shade, root strength (reinforcement of stream banks from erosion), and leaf litter fall functions of
stream riparian area. Although an increase in salmonid productivity over existing conditions (estimated as
30% of potential productivity at 100% functionality) can be expected to occur, it is unlikely to reach or
exceed the 60% of potential productivity level of streams traversing rural-residential landcover. A period of
at least 80 years would be required in Alternative 2 for the forested portion of the buffer to reach a mature
state and provide the maximum benefit possible for a buffer under 56 feet in width (
or creation of forested riparian buffers, has the potential of producing significant improvements in salmonid
production capacity in study area streams within 3 to 4 years. The low coho parr densities recorded in index
reaches before stream rehabilitation activities indicates that the baseline productivity of these streams was
probably similar to streams traversing agricultural land cover (approximately 30% or less of 100%
functionality). Both streams experienced close to a 100% increase in coho parr densities. This would
represent an increase to approximately 80% of production at full functionality. Although it is likely that some
of this increase may be due to a redistribution of fish within the systems or natural fluctuations in site-specific
density of coho parr, these studies suggest that active management of stream and riparian habitat (which in
this case did not include management of the riparian vegetation) has the potential to restore salmonid
production capacity to levels between 60% and 80% of full functionality in a relatively short period of time
compared to the length of time required to restore a riparian buffer of mature conifer forest (or mixed forest
dominated by conifers).

A lack of suitable seed sources, invasive weeds, destruction of seedlings by rodents and deer, livestock
grazing within riparian zones, and other factors can delay or completely prevent normal forest succession
from occurring in Alternative 4. While some researchers see active management as only marginally effective
and call for wide (e.g., site potential tree height) unmanaged buffers to deliver old-growth equivalent large
wood supplies over long periods of time, the desire to improve instream conditions within shorter time frames
motivates active management for the near term (Berg 2003). In addition, if wide unmanaged buffer cannot
regenerate a mature forest without active intervention (i.e. management), the expected long-term benefits of
wide buffers will not be achieved. Assuming a wide (>131 feet) forested riparian buffer dominated by
conifers can be grown within an unmanaged buffer, stream functionality is likely to eventually reach and
exceed 80% of a fully functioning forested landscape (Beechie et al. 2003). It is unlikely that 100%
functionality will be reached because land use outside of the forested riparian buffer will increase impervious
surface area, drainage networks, and peak flows. It will take at least 80 years to generate a mature, conifer
dominated forested buffer and this is likely to occur within the 80 year time frame only if active management
is used to replant and allow the speedy regeneration of a riparian forest. In the absence of active
management, it will take far longer (or be impossible) to produce the mature riparian forest necessary to
restore stream functions and salmonid production capacity in study area streams.

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Pess, G., D.R. Montgomery, T.J. Beechie, and L. Holsinger. 2003. “Anthropogenic Alterations to the
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Salo, E.O. 1991. “Life History of Chum Salmon (Oncorhynchus keta ).” In Pacific Salmon Life Histories.
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