Malheur River Subbasin Assessment and Management Plan For Fish and Wildlife Mitigation Appendix A, Part 2 – Aquatic Assessment Malheur Watershed Council And Burns Paiute Tribe May, 2004 Prepared with assistance of: Watershed Professionals Network, LLC Malheur River Subbasin Assessment and Management Plan For Fish and Wildlife Mitigation Appendix A, Part 2 –Assessment Aquatic 1 INTRODUCTION...................................................................................................... 7 2 FOCAL SPECIES CHARACTERIZATION AND STATUS ...................................... 8 2.1 NATIVE AND NON-NATIVE FISH AND WILDLIFE SPECIES OF ECOLOGICAL IMPORTANCE .......................8 2.1.1 Pacific lamprey ........................................................................................................................8 2.1.2 Mountain whitefish...................................................................................................................8 2.1.3 Other fish species....................................................................................................................8 2.2 BULL TROUT (SALVELINUS CONFLUENTUS): CURRENT POPULATION DATA AND STATUS...................10 2.2.1 Bull Trout: Abundance...........................................................................................................11 2.2.2 Bull Trout: Capacity ...............................................................................................................13 2.2.3 Bull Trout: Productivity ..........................................................................................................14 2.2.4 Bull Trout: Life History Diversity ............................................................................................14 2.2.5 Bull Trout: Carrying Capacity ................................................................................................15 2.2.6 Bull Trout: Population Trend and Risk Assessment..............................................................17 2.2.7 Bull Trout: Unique Population Units ......................................................................................18 2.2.8 Bull Trout: Life History Characteristics of Unique Populations..............................................18 2.2.9 Bull Trout: Genetic Integrity of Unique Populations ..............................................................20 2.2.10 Bull Trout: Estimate of Historic Status ..............................................................................21 2.3 BULL TROUT DISTRIBUTION ..........................................................................................................22 2.3.1 Bull Trout: Current Distribution/Spatial Diversity...................................................................22 2.3.2 Bull Trout: Historic Distribution..............................................................................................24 2.3.3 Bull Trout: Identification of Differences in Distribution Due to Human Disturbance..............24 2.4 REDBAND TROUT (ONCORHYNCHUS MYKISS): CURRENT POPULATION DATA AND STATUS ...............25 2.4.1 Redband Trout: Abundance ..................................................................................................25 2.4.2 Redband Trout: Capacity ......................................................................................................27 2.4.3 Redband Trout: Productivity..................................................................................................28 2.4.4 Redband Trout: Life History Diversity ...................................................................................28 2.4.5 Carrying Capacity..................................................................................................................29 2.4.6 Redband Trout: Population Trend and Risk Assessment .....................................................31 2.4.7 Redband Trout: Unique Population Units..............................................................................31 2.4.8 Redband Trout: Life History Characteristics of Unique Populations.....................................31 2.4.9 Redband Trout: Genetic Integrity of Unique Populations......................................................32 2.4.10 Redband Trout: Estimate of Historic Status......................................................................32 2.5 REDBAND TROUT DISTRIBUTION ...................................................................................................34 2.5.1 Redband Trout: Current Distribution/spatial Diversity...........................................................34 2.5.2 Redband Trout: Historic Distribution .....................................................................................35 2.5.3 Redband Trout: Identification of Differences in Distribution Due to Human Disturbance .....35 2.6 CHINOOK SALMON (ONCORHYNCHUS TSHAWYTSCHA): CURRENT POPULATION DATA AND STATUS ..37 2.6.1 Chinook Salmon: Abundance................................................................................................37 2.6.2 Chinook Salmon: Capacity ....................................................................................................37 2.6.3 Chinook Salmon: Productivity ...............................................................................................37 2.6.4 Chinook Salmon: Life History Diversity .................................................................................38 2.6.5 Chinook Salmon: Carrying Capacity .....................................................................................38 Malheur River Subbasin i Management Plan May, 2004 2.6.6 Chinook Salmon: Population Trend and Risk Assessment...................................................39 2.6.7 Chinook Salmon: Unique Population Units ...........................................................................40 2.6.8 Chinook Salmon: Life History Characteristics of Unique Populations...................................40 2.6.9 Chinook Salmon: Genetic Integrity of Unique Populations ...................................................40 2.6.10 Chinook Salmon: Estimate of Historic Status ..................................................................41 2.7 CHINOOK SALMON DISTRIBUTION..................................................................................................42 2.7.1 Chinook Salmon: Current Distribution/spatial Diversity.........................................................42 2.7.2 Chinook Salmon: Historic Distribution...................................................................................42 2.7.3 Chinook Salmon: Identification of Differences in Distribution Due to Human Disturbance...43 2.8 DESCRIPTION OF AQUATIC INTRODUCTIONS, ARTIFICIAL PRODUCTION AND CAPTIVE BREEDING PROGRAMS ...............................................................................................................................................44 2.8.1 Aquatic Introductions: Current Situation................................................................................44 2.8.2 Aquatic Introductions: Historic Situation................................................................................45 2.8.3 Aquatic Introductions: Affect of Straying/Ecologic Consequences .......................................45 2.8.4 Artificial Production: Current..................................................................................................46 2.8.5 Artificial Production: Historic..................................................................................................46 2.8.6 Artificial Production: Affect of Straying/ecologic Consequences...........................................46 2.8.7 Relationship Between Naturally and Artificially-Produced Populations ................................47 2.9 HARVEST IN THE SUBBASIN...........................................................................................................48 3 AQUATIC ASSESSMENT ..................................................................................... 50 3.1 OVERVIEW OF QHA METHODOLOGY..............................................................................................51 3.1.1 Subbasin Effects Not Addressed by QHA.............................................................................53 3.2 REACH SELECTION AND FOCAL SPECIES RANGE ...........................................................................54 3.3 CURRENT AND HISTORIC HABITAT CONDITIONS .............................................................................55 3.4 AQUATIC SPECIES HYPOTHESIS....................................................................................................58 3.5 REFERENCE AND CURRENT CONDITIONS, AND LIMITING FACTORS, AT THE WATERSHED SCALE .......61 3.5.1 Main Malheur Watershed1 ....................................................................................................61 3.5.2 Upper Malheur Watershed ....................................................................................................71 3.5.3 Willow Creek Watershed .......................................................................................................79 3.5.4 Bully Creek Watershed..........................................................................................................84 3.5.5 North Fork Malheur Watershed.............................................................................................91 3.5.6 South Fork Malheur Watershed ............................................................................................97 3.6 SUMMARY