Editor Stacey H. Stovall, Conservation Innovations, Inc. Subbasin Team Leader

Background 1

Introduction 2

Subbasin Description 3

General Location 3

Drainage Area 3

Topography/geomorphology 4

Climate 7

Major Land Uses 8

Water Resources Development and Operations 12

Hydrology 19

Water Quality 23

Vegetation 28

Fish and Wildlife Resources 39

Fish and Wildlife Status 39

Habitat Areas and Quality 81

Watershed Assessment 94

Major Limiting Factors 97

Artificial Production 103

Existing and Past Efforts 103

Subbasin Management 109

Existing Plans, Policies, and Guidelines 109

Goals, Objectives, Strategies, and Recommended Actions 124

Research, Monitoring and Evaluation Activities 141

Statement of Fish and Wildlife Needs 147

Boise/Weiser/Payette Subbasin Recommendations 154

Projects and Budgets 154

Research, Monitoring and Evaluation Activities 173

Needed Future Actions 185

Statement of Fish and Wildlife Needs 190

Actions by Others 196

References 211

Table 1. Geology of the Boise-Payette-Weiser subbasins. The percent occurrence of major geologic mapping units is summarized by watershed (adapted from Bond and Wood 1978; Jensen et al. 1997). 6

Table 2. Climatic regimes of watersheds within the Boise-Payette-Weiser subbasins: the proportional representation of varying climatic regimes (using the Koppen climatic classification system, described by Godfrey 1999) within the subbasins is summarized by watershed. 8

Table 3. Summary of land ownership patterns within the Boise-Payette-Weiser subbasins: the percent representation of land ownership class is listed for each watershed. 9

Table 4. Land use patterns within the watersheds of the Boise-Payette-Weiser subbasins: the percent representation of levels of ecological modification is listed by watershed. 9

Table 5. Distribution of forest and rangeland related land uses among land ownership classes within the Boise-Payette-Weiser subbasins. 10

Table 6. Summary of USFS inventoried roadless areas within the Boise-Payette-Weiser subbasins. Roadless areas are listed with X’s indicating their distribution within subbasin watersheds. 11

Table 7. Summary of Boise Project operating activities. Adopted from BOR (1996). 14

Table 8. Summary of Payette system reservoir operating activities. Adopted from BOR (1996). 14

Table 9. Summary of Boise and Payette River flow augmentation volume provided by BOR, 1991 - 2001. Adopted from Leitzinger (2000). 15

Table 10. Existing licensed instream flow water rights for the Boise and Payette River subbasins. 20

Table 11. Existing recommended licensed instream flow water rights for the Boise and Payette River subbasins. 20

Table 12. Recommended pool elevations (KAF) and flows (cfs) for fisheries in the Boise and Payette River subbasins. Adapted from BOR (1998). 21

Table 13. Water quality limited segments found on Idaho's 1998 303(d) list in the Boise, Payette, and Weiser River subbasins. 25

Table 14. Percent representation of 14 PNV plant association groups within the Boise-Payette-Weiser subbasins is listed by major watershed (adapted from Jensen et al. 1997). 29

Table 15. Percent representation of 29 land cover classes within the Boise-Payette-Weiser subbasins is listed by watershed (adapted from Landscape Dynamics Lab 1999). 30

Table 16. Matrix of differences between current versus modeled historic fire disturbance regimes in the Boise-Payette-Weiser subbasins (adopted from Hann et al. 1997). Values appearing as “0.0” are less than 0.1 percent. 33

Table 17. Rare and endemic plant species (with global rank G1 through G3 or state rank S1 through S2) known to occur within the Boise-Payette-Weiser subbasins are listed by species with the number of population occurrences summarized by watershed. 36

Table 18. Noxious weed species distributions within the Boise-Payette-Weiser subbasins are summarized by county. Data are taken from Morishita et al. (2001) with supplemental information from field contacts. 38

Table 19. Fish species documented to be present in the Boise-Payette-Weiser subbasins, Idaho. 40

Table 20. Fish population and density estimates for wild rainbow trout and mountain whitefish in a one-mile reach of the South Fork Boise River upstream of Deadwood Creek. Data collected by the IDFG in 1991, 1994, and 1998. 43

Table 21. Fish species sampled using electrofishing gear in tributaries of the upper South Fork Boise River in 1998. Data collected by the IDFG (Partridge and Warren, in press). 44

Table 22. Densities and population estimates of wild rainbow trout collected while electrofishing in the Yuba River drainage in July 2000. 45

Table 23. Densities of redband trout observed while snorkeling in the Yuba River drainage on July 25, 2000. Data are from the IDFG. 45

Table 24. Summary of snorkel surveys in select tributaries of the North Fork Payette River drainage (Faurot 2001). 51

Table 25. Wildlife species documented to occur within the Boise-Payette-Weiser subbasins, including current state and federal status for threatened, endangered, and special status species (Idaho Conservation Data Center, IDFG). 61

Table 26. Documented occurrences of threatened, endangered, or otherwise rare animal species within the Boise-Payette-Weiser subbasins, Idaho. Federally listed species are identified in bold. Information provided by the Idaho Conservation Data Center. 68

Table 27. Bald eagle nest territories within the Boise-Payette-Weiser subbasins, Idaho. 71

Table 28. Elk population status and IDFG objectives for game management units within the Boise-Payette-Weiser subbasins (Revised 8/21/01). 73

Table 29. Deer population status and IDFG objectives for game management units within the Boise-Payette-Weiser subbasins (Revised 8/21/01). 74

Table 30. Densities of rainbow trout and bull trout observed using snorkeling techniques in the Middle Fork Boise River in 1988, 1993, and 2000. 85

Table 31. Wildlife habitat areas in the Boise-Payette-Weiser subbasins, Idaho. 93

Table 32. Recommended pool elevations (KAF) and flows (cfs) for fisheries in the Boise and Payette River subbasins. Adapted from BOR (1998). 113

Table 33. Existing licensed instream flow water rights for the Boise and Payette River subbasins. 120

Table 34. Instream flow regimes recommended by the IDFG for the Boise-Payette-Weiser subbasins. 121

Table 35. NAQWA sites in the Upper Middle Snake River subbasin. 176

Table 36. BURP monitoring sites and TMDL schedule in the Upper Mid Snake River Subbasin. 178

Table 37. Subbasin Summary FY 2003 - Funding Proposal Matrix 202

Figure 1. Bull trout distribution in the Boise River subbasin, Idaho. 41

Figure 2. Redband trout distribution in the Boise River subbasin, Idaho. 42

Figure 3. Bull trout distribution in the Payette River subbasin, Idaho. 48

Figure 4. Redband trout distribution in the Payette River subbasin, Idaho. 49

Figure 5. Bull trout presence in the Weiser River subbasin, Idaho. 56

Figure 6. Redband trout presence in the Weiser River subbasin, Idaho. 57