Subbasin incubation

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					                                            Supplementary Tables

Table S1. Empirical water temperature data during the pre-spawning period.

                                                                                           Mean pre-spawning
 Basin               Subbasin                                           Gage                 temperature
                                                                                                 (°C)
 Snohomish           Coal Creek - Upper                                07D130                       17.7
 Snohomish           Quilceda Creek                                    QCMF                         14.8
 Snohomish           Skykomish River - Lower Mainstem                  07C070                       18.1
 Snohomish           Snohomish Estuary                                   Dd                         18.7
 Snohomish           Snoqualmie River - Mouth                          07D050                       19.0
 Snohomish           Sultan River - Lower                             12138160                      11.8
 Snohomish           Tolt River - South Fork Above Dam                12147600                      13.8
 Snohomish           Tolt River - South Fork Below Dam                12148300                      12.7
 Stillaguamish       French - Segelsen                                 05B110                       16.3
 Stillaguamish       Stillaguamish River - Lower                       05A070                       19.7
 Stillaguamish       Stillaguamish - Lower North Fork                  05B070                       18.8
 Stillaguamish       Stillaguamish - Lower South Fork                  05A090                       20.2
 Sammamish           North Creek                                  North Cr @ 196th                  15.5
 Sammamish           Swamp Creek                                 Swamp Cr nr 228th                  16.9


Notes: The U.S. Geological Survey, Washington Department of Ecology, and Snohomish County Surface Water

Management Division oversee gages in and around the Snohomish River basin that record water temperature every

hour or 30 minutes. These gages have operated intermittently since the 1980s. To ensure that gages used in this

analysis operated during equivalent time frames, we trimmed the data to temperatures from 2001–2003, which was

the longest time window with the largest number of gages operating simultaneously (14 gages). For each of these

gages, we defined pre-spawning temperature as the mean of the maximum daily temperatures from 15 July to 15

August during 2001–2003. We defined temperature this way for two reasons: first, because the functional

relationship linking pre-spawning temperature and Chinook survival in SHIRAZ defined pre-spawning temperature

as the mean of the daily maximum temperatures during the month of June (Cramer 2001) and, second, because the

pre-spawning period in the Snohomish River basin does not begin until mid-July (PNRBC 1981).




                                                   S-1
Table S2. Empirical water temperature data during the incubation period.

                                                                                                        Mean
                                                                                                     incubation
 Basin             Subbasin                                                 Gage
                                                                                                    temperature
                                                                                                        (°C)
 Snohomish         Allen Creek                                         Allen Cr @ 55th                   9.7
 Snohomish         Beckler River                                           Beckler                       5.7
 Snohomish         Fobes Hill                                         Mosher Cr @ 36th                   7.5
 Snohomish         French Creek                                    French Cr @ 167th Av                  7.1
 Snohomish         May Creek / Wallace River - Lower                       Wallace                       7.6
 Snohomish         Quilceda Creek                              Quilceda Cr MF @ 51st Av NE               8.2
 Snohomish         Skykomish River - Lower North Fork                   Sky lower NF                     6.2
 Snohomish         Skykomish River - South Fork                            Sky SF                        6.2
 Snohomish         Skykomish River - Upper South Fork                   Sky upper SF                     5.7
 Snohomish         Snohomish Estuary                         Ebey Slough @ Drainage District 6           7.9
 Snohomish         Sultan River - Lower                                   12137800                       7.2
 Snohomish         Sunnyside Drainages                                Fox Cr @ SR204                     8.1
 Snohomish         Tolt River - North Fork                                12147500                       6.7
 Snohomish         Tolt River - South Fork Above Dam                      12147600                       4.8
 Snohomish         Tolt River - South Fork Below Dam                      12148300                       7.2
 Sammamish         Little Bear Creek                             Little Bear Cr @ 51st St SE             8.0
 Sammamish         North Creek                                        North Cr @ 196th                   7.2
 Sammamish         Swamp Creek                                       Swamp Cr nr 228th                   7.5

Notes: Data were derived from 18 gages programmed to measure water temperature every hour or 30 minutes in the

Snohomish and Sammamish River basins. The gages were managed by the Northwest Fisheries Science Center,

USGS, and Snohomish County SWM. Because fewer gages were deployed during the incubation period than during

the pre-spawning period, it was necessary to include gages that were not always operating simultaneously in order to

ensure an adequate sample size. For each gage, we found the mean of the daily mean temperatures for each month

during a given incubation period. Then we averaged those monthly means across all incubation periods on record

from the 1990 water year onward.




                                                   S-2
Table S3. Empirical peak flow data during the incubation period.


                                                                                                 Mean peak flow
 Basin             Subbasin                                                  Gage
                                                                                                    (m3∙s-1)

 Snohomish         Cathcart Drainages - Upper Snohomish                    12150800                   1531.3
 Snohomish         Coal Creek - Lower                                      12144500                   587.3
 Snohomish         French Creek                                     French Cr @ 167th Ave               4.5
 Snohomish         Pilchuck River - Lower                                  12155300                    91.4
 Snohomish         Quilceda Creek                                   WF Quilceda @ 116th St              2.8
 Snohomish         Raging River                                            12145500                    39.9
 Snohomish         Skykomish River - Upper Mainstem                        12134500                   928.9
 Snohomish         Snoqualmie River - Lower Middle Fork                    12141300                   319.4
 Snohomish         Snoqualmie River - Lower North Fork                     12142000                   138.0
 Snohomish         Snoqualmie River - Lower South Fork                     12144000                   118.3
 Snohomish         Snoqualmie River - Mid-Mainstem                         12149000                   738.5
 Snohomish         Snoqualmie River - Upper South Fork                     12143400                    75.5
 Snohomish         Sultan River - Upper                                    12137290                    37.7
 Snohomish         Tolt River - Lower                                      12148500                   108.1
 Snohomish         Tolt River - North Fork                                 12147500                    81.6
 Snohomish         Tolt River - South Fork Above Dam                       12147600                    19.5
 Skagit            Sauk River                                              12189500                   819.1
 Stillaguamish     Stillaguamish River - Lower North Fork                  12167000                   503.6
 Sammamish         North Creek                                      North Cr @ County line             14.2
 Sammamish         Swamp Creek                                          Swamp Cr @ I-405                5.2

Notes: Flow data were derived from 20 gages managed by USGS and Snohomish County SWM. Each gage

operated continuously during the incubation periods from 1995 to 2003, ensuring that peak flows measured during

this time frame at different gages were comparable. We defined peak flow (Q), for a given incubation period (i), as

the largest daily mean flow occurring during that period at a particular gage (j). Then we calculated the mean peak

flow for each gage during the 1995–2003 time frame:

                                                             8
                                                             Q j
                                                mean Q j  i 1     ,
                                                               8

where i = 1 and i = 8 represented the 1995–1996 and 2002–2003 incubation periods, respectively.



                                                   S-3
Table S4. Empirical fine sediment data.

                                                                             Number of              Mean % fines
 Basin                  Subbasin
                                                                             data points             < ~ 6.3 mm

 Snohomish              Allen Creek                                               4                      55.3
 Snohomish              Coal Creek - Lower                                        3                      51.0
 Snohomish              Coal Creek - Upper                                        1                      50.8
 Snohomish              Fobes Hill                                                1                      72.8
 Snohomish              French Creek                                              40                     25.6
 Snohomish              Lake Stevens Drainages                                    13                     78.8
 Snohomish              May Creek / Wallace River - Lower                         1                       5.1
 Snohomish              Pilchuck River - Lower                                    9                      12.4
 Snohomish              Quilceda Creek                                            15                     75.7
 Snohomish              Raging River                                              2                      26.5
 Snohomish              Skykomish River - Upper North Fork                        11                      3.5
 Snohomish              Snoqualmie River - Lower South Fork                       4                      25.7
 Snohomish              Snoqualmie River - Mid-Mainstem                           21                     62.2
 Snohomish              Snoqualmie River - Mouth                                  4                      99.0
 Snohomish              Snoqualmie River - Upper Mainstem                         13                     49.4
 Snohomish              Sunnyside Drainages                                       6                      29.3
 Snohomish              Tokul Creek                                               2                      12.5
 Snohomish              Tolt River - South Fork Below Dam                         1                      10.0
 Snohomish              Tulalip and Battle Creeks                                 1                      48.6
 Stillaguamish          Boulder River                                             4                       5.5
 Stillaguamish          Canyon Creek - Lower                                      8                      18.3
 Stillaguamish          Canyon Creek - Upper                                      5                       6.1
 Stillaguamish          French - Segelsen                                         9                      11.4
 Stillaguamish          Squire Creek                                              6                       5.1
 Stillaguamish          Stillaguamish River - Lower North Fork                    29                     27.9
 Stillaguamish          Stillaguamish River - Middle North Fork                   8                      17.3
 Stillaguamish          Stillaguamish Canyon                                      12                     70.4

Notes: Fines were defined as the fraction of streambed sediments with diameters < ~6.3 mm. This diameter was

chosen because most local fines data were reported in this size fraction, and because this size fraction was linked

empirically to Chinook survival (Tappel and Bjornn 1983). Data were derived from Booth et al. 1991, DeVries et

al. 2001, Parametrix Inc., Perkins Geosciences, Earth Systems, and Harper Houf Righellis Inc. 2001, and Snohomish

County SWM 2002. In subbasins with more than one data point, the mean percent fines value was calculated.



                                                     S-4
                                   Supplementary References

Booth, D.B., Bell, K., and Whipple, K.X. 1991. Sediment transport along the South Fork and

       mainstem of the Snoqualmie River. King County Surface Water Management Division,

       Basin Planning Program, Seattle, WA.

Cramer, S.P. 2001. The relationship of stream habitat features to potential for production of four

       salmonid species. Report prepared for the Oregon Building Industry Association by S.P.

       Cramer & Associates, Inc., Gresham, OR.

DeVries, P., McHugh, M., Beamer, E., Pess, G., and Glasgow, J. 2001. Monitoring and assessing

       fine sediment intrusion as a function of scour depth and sediment loading. Washington

       Trout/Washington State Department of Ecology, Seattle, WA.

Pacific Northwest River Basins Commission (PNRBC). 1981. Snohomish River basin resource

       management program. Main report prepared by the Snohomish Study Team, Vancouver,

       WA.

Parametrix, Inc., Perkins Geosciences, Earth Systems, and Harper Houf Righellis, Inc. 2001.

       Lower Tolt River floodplain reconnection site analysis. Final draft report prepared for

       Seattle City Light and King County Department of Natural Resources.

Snohomish County Surface Water Management (SWM). 2002. Aquatic habitat summary: a

       regional summary of the DNR habitat survey of urban and urbanizing streams of

       Snohomish County. Snohomish County Public Works Department, Surface Water

       Management Division, Everett, WA.

Tappel, P.D., and Bjornn, T.C. 1983. A new method of relating size of spawning gravel to

       salmonid embryo survival. N. Am. J. Fish. Manag. 3:123-135.




                                            S-5

				
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Description: Subbasin incubation