United States Department of Agriculture Forest Service Pacific Southwest Region AQUATIC RESOURCES BIOLOGICAL ASSESSMENT BIOLOGICAL EVALUATION

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1 United States Department of Agriculture Forest Service Pacific Southwest Region AQUATIC RESOURCES BIOLOGICAL ASSESSMENT BIOLOGICAL EVALUATION TROUT CREEK RESTORATION PROJECT Shasta McCloud Management Unit Shasta-Trinity National Forest Siskiyou County, California July 19, 2005 Prepared by: oseph Z ak Fisheries Biologist Reviewed by: William Brock Forest Fisheries Biologist Date: /ter' Date: Approved by: J Michael Hupp District Ranger f Date:

2 c: TROUT CREEK RESTORATION PROJECT AQUATIC RESOURCES BIOLOGICAL ASSESSMENT/BIOLOGICAL EVALUATION SHASTA MCCLOUD MANAGEMENT UNIT SHASTA-TRINITY NATIONAL FOREST PROJECT LOCATION A 1.5 mile reach of Trout Creek, located approximately 20 miles northeast of McCloud, Siskiyou County, California T4IN, R1E, Sections 6, and T42N, RIE, Section 31. MDM. 0

3 EXECUTIVE SUMMARY OF BIOLOGICAL ASSESSMENTIE VALUATION FOR THE TROUT CREEK RESTORATION PROJECT DATE: July 19, 2005 PROJECT NAME: Trout Creek Restoration Project NAME OF PREPARER: Joseph Zustak TES SPECIES SPECIES PRESENT MANAGEMENT EFFECTS STATUS IN REQUIREMENTS, DETERMINATION REASONS OR PROJECT STANDARDS, MITIGATION FOR NO AREA GUIDELINES, EFFECT Habitat or SPECIES SPECIFIC PROJECT detections DESIGN STANDARDS L^ Central Valley T No No effect No Suitable habitat steelhead Coho salmon T No No effect No suitable habitat Delta smelt T No No effect No suitable habitat Shasta cra y fish E No No effect No suitable habitat Vernal pool fairy T No No effect No suitable habitat shrimp Vernal pool tadpole E No No effect No suitable habitat shrimp Winter-run chi nook E No No effect No suitable habitat salmon Central Valley spring- T No No effect No suitable habitat run chinook Northern California T No No effect No suitable habitat steelhead California floater S No No effect No suitable habitat Klamath mts, Province S No No effect No suitable habitat steelhead Montain eaciam S No No effect No suitable habitat Hardhead minnow S No No effect No suitable habitat McCloud River redhand trout S Yes May affect'nlaa* Conduct fish rescue Avoid spawning season Upper Klatnath/Trinity S No No effect No suitable habitat chinook s rin g-run Upper Trinity River S No No effect No suitable habitat chinook fall-run Nugget pebblesnail S No No effect No suitable habitat Scalloped Ju a S No No effect No suitable habitat *May affect/nlaa: May affect individuals, but is not likely to adversely affect the species nor result in a trend towards federal listing or loss of viability for this species within the planning area of the Shasta- Trinity National Forest. In the absence of a rangewide viability assessment, this determination is based on local knowledge of the species and professional judgement.

4 I. INTRODUCTION A Biological Assessment (BA) is the means by which a determination is made whether a proposed federal action may or may not have an effect on any threatened or endangered species and/or its habitat. A Biological Evaluation (BE) is the means by which a determination is made whether a proposed federal action may or may not have an impact on a Forest Service (FS) Sensitive species and/or its habitat. This BA / BE is prepared in accordance with the legal requirements set forth under section 7 of the Endangered Species Act (19 U.S.C.1536 (c)) and follows the standards established in Forest Service Manual direction, FSM (USDA 1991). The purpose of this BABE is to analyze, in sufficient detail, the potential effects of whether the proposed Trout Creek Restoration Project may or may not have effects upon any threatened, endangered, and / or Forest Service sensitive species and / or its habitat. Aquatic species including frogs, salamanders and turtles are addressed in a separate document. Survey and Manage animal species identified within the Record of Decision / Standards &, Guidelines for Amendments to the Survey and Manage, Protection Buffer, and other Mitigation Measures Standards and Guidelines (USDA/USDI 2001) are no longer addressed as this requirement has been removed. Section 7 of the Endangered Species Act (ESA, 19 U.S.C (c)), as amended (1978, 1979, 1982) directs federal agencies to ensure that actions authorized, funded, or carried out by them are not likely to jeopardize the continued existence of any species listed or proposed for listing as threatened or endangered, or result in destruction or adverse modification of their critical habitats (16 U.S.C et seq.). Federal Agencies must consult with the appropriate Secretary whenever an action is likely to. affect a species listed as threatened or endangered, or to affect its critical habitat. The act mandates conference with the appropriate Secretary whenever an action is likely to jeopardize the continued existence of any species proposed for listing as threatened or endangered, or whenever an action might result in destruction or adverse modification of critical habitat proposed for listing (16 U.S.C (a) 4). A. AREA OF ANALYSIS The legal location of the project is T41N, RI E, Section 6, and T42N., RI E., Section 31. MDM. The area of analysis will include 1.5 miles of Trout Creek located approximately 20 miles northeast of McCloud, California in the Upper McCloud River Basin. A site map can be found in the project proposal. B. THREATENED, ENDANGERED AND SENSITIVE SPECIES 1. Threatened and Endangered Species USFWS Sacramento Office Website Updated 6/20/05 and National Marine Fisheries Service Salmonid Species List as per 7/19/05 (wildlife species are discussed in a separate document)

5 The following list fulfills the requirements to provide a current species list pursuant to Section 7 (c) of the Endangered Species Act, as amended. CRITICAL SCIENTIFIC NAME COMMON NAME CATEGORY HABITAT Oncorhynchus mykiss Central Valley steelhead T P Oncorhynchus kisutch Coho salmon, SONCC T Y Hypomesus transpacifcus Delta smelt T N Oncorhynchus tshawyscha Winter-run Chinook salmon E N Pacifastacus fortis Shasta crayfish E N Branchinecta lvnchi Vernal pool fairy shrimp T N Lepidus packardi Vernal pool tadpole shrimp E N Oncorhvnchus tshawtiwtscha Central Valley spring-run T P Chinook salmon Oncorhvnchus mvkiss Northern Calif. Steelhead T N (E) Endangered (T) Threatened (P) Proposed Critical Habitat Listed in the Federal Register as being in danger of extinction Listed as likely to become endangered within the foreseeable future. Proposed for listing under the T&E act Y Designated, P Proposed, N=None Designated 2. Forest Service Reeional Office April 2004 Sensitive Animal Species for the Shasta-Trinit y NF (wildlife species are discussed in a separate document) C: Hardhead minnow (Mvlophar odan conocephalus) McCloud River redband trout (Oncorh y nchus mykiss, pop 7) Upper Klamath/Trinity Chinook salmon spring-run (Oncorhvnchus tshawytscha) Upper Trinity River Chinook salmon fall-run (Oncorhynchus tshawytscha) Klamath Mtn. Province steelhead (Oncorh y nchus mykiss) California floater (Anodonta californiensis) Scalloped Juga (Juga occata) Nugget pebblesnail (Fluminicola seminalis) Montane peaclam (Psidium ultramontanum)

6 0 II. CONSULTATION TO DATE An updated species list for the project area (Rainbow Mountain 7.5 minute quad) was obtained on July 19, 2005 from the internet website from the Sacramento Field Office. The list, updated to June 20, 2005 fulfills the requirement of the Fish and Wildlife Service to provide a species list pursuant to Section 7 of the Endangered Species Act, as amended. The U.S. Fish and Wildlife Service was contacted concerning the effects of the proposed project on listed species. Danielle Chi of the U.S. Fish and Wildlife Service, Red Bluff Office was informally consulted during a visit to Trout Creek in September 2001 regarding this project. III. CURRENT MANAGEMENT DIRECTION Current management direction for maintaining the viability of threatened, endangered, and sensitive species and their habitats can be found in the Shasta-Trinity National Forest Land and Resource Management Plan (LRMP; USDA 1995). Standards and guidelines for proposed actions must also be consistent with the Northwest Forest Plan Record of Decision (ROD 1994). The Forest LRMP includes this area as the `McCloud Flats Management Area 2'. Almost all of the project area lies within the `matrix prescription 8' designation which prescribes a commercial wood products emphasis. About 5% of the area lies in matrix prescription 6 (wildlife habitat management). The management direction for Trout Creek is also guided by the Upper McCoud River Redband Trout Conservation Agreement, IV. DESCRIPTION OF PROPOSED ACTION The Trout Creek Restoration Project has been identified as an opportunity to improve redband trout habitat by restoring the stream to the historic channel. This would restore the connectivity of Trout Creek with the surrounding meadow complex in an area where the present channel has downcut to a large gully. Redband trout habitat condition is very poor in this area as it is difficult to establish riparian vegetation. Habitat complexity is also very low. A detailed description of the proposed action can be found in the Trout Creek Restoration Project Environmental Assessment. V. EXISTING ENVIRONMENT Threatened and Endangered Species The proposed project will not affect any listed species because the present range of these species lies outside of the project area. Central Valley steelhead (Oncorhynchus mykiss) Coho salmon (Oncorhynchus kisutch) Delta smelt (Hypomesus transpacificus) Winter-run chinook salmon (Oncorhynchus tshaw y tscha) Central Valley spring-run chinook (Oncorhynchus tshawytscha)

7 Northern California steelhead (Oncorhynchus mykiss) Shasta crayfish (Pacifastascus fortis) Vernal pool fairy shrimp (Branchinecta lynchi) Vernal pool tadpole shrimp (Lepidus packardi) Central Valley Steelhead The Central Valley steelhead is an evolutionarily significant unit (ESU) of steelhead found in the rivers of the central valley of California. Nonmigratory populations of rainbow trout, not of hatchery origin, belong to this ESU, as would populations of presumably "residualized" steelhead that live in reservoirs and migrate into tributaries to spawn (Moyle, 2002). Shasta lake has been stocked with hatchery trout since it's creation: 120,000 trout per year since This most likely has resulted in a severe contamination of the steelhead gene pool such that it is unlikely that any recognizable "residualized" steelhead exist within the lake. Additionally, there is no suitable habitat within the proposed project area and these streams are not accessable during the time rainbow trout spawning. This species is dropped from further consideratin. Coho Salmon Coho salmon once spawned in the upper Sacramento River and are believed to have spawned within the McCloud River as well. This species no longer occurs within this area as Shasta Darn effectivel y cuts off access to all it's former habitat upstream from the dam. This species was once introduced to Shasta lake in the mid-1960s, in an effort to develop a landlocked population. This program was discontinued shortly thereafter due to unreliable sources of eggs. This population has since died out. This species is dropped from futher consideration. _. Delta Smelt Delta smelt are endemic to the upper San Francisco Estuary, principally the Delta and Suisun Bay (Moyle, 2002). The occurrence of this species is well outside of the proposed project area and as such is dropped from further consideration. Winter-run Chinook Salmon This unique run is listed as Endangered by both Federal and State governments. It is endangered because Shasta Dam completely blocked the run from accessing historical spawning grounds (Moyle, 2002) It now persists in about 70 km of river below Keswick dam. As this run no longer exists within the proposed project area it has been removed from further consideration. Central Valley Spring-Run Chinook Salmon Spring-run Chinook salmon in the Sacramento-San Joaquin River system historically made up one of the largest salmon runs on the Pacific coast. The decline of the spring-run Chinook began when streams were disrupted by mining and irrigation diversion. The decline was rendered complete following the construction of Shasta Dam in 1944 (Moyle, 2002). The dam resulted in the loss of at least 250 km of habitat as these salmon were no longer able to access this area. This species therefore no longer occurs

8 within the proposed project area and is removed from further consideration. Northern California Steelhead These steelhead inhabit the northcoast streams of California. They are still widespread, but their numbers continue to decline. These fish were listed as Threatened by NMFS in This species does not occur within the project area. They have been removed from further consideration. The Magnuson-Stevens Fishery Conservation Management Act (MSFCMA), as amended by the Sustainable Fisheries Act of 1996 (public Law ), requires all federal agencies to consult with the National Marine Fisheries Service division of the National Oceanographic and Atmospheric Administration (NOAA Fisheries) on all actions or proposed actions (permitted, funded, or undertaken by the agency) that may adversely affect Essential Fish Habitat. Essential Fish Habitat (EFH) is defined as those waters and substrate necessary to fish for spawning, breeding, feeding, and growth to maturity. EFH consultation is being. consolidated with ESA consultation based upon the finding by NOAA Fisheries that the ESA Section 7 consultation process used by the Forest Service can also be used to satisfy EFH consultation. In this regard, this BA also serves the purpose of the EFH assessment, and will include all of the fish species addressed in this BA as per the ESA. Based on the information provided above for all of the historically anadromous salmonid fish species, EFH will not be addressed further in this document. This conclusion is made due to the construction of Shasta Dam rendering all historic EFH habitats inaccessible anywhere near the proposed project area. Shasta Crayfish The Shasta crayfish is the only surviving crayfish native to California. It has a distribution that is limited to the mid-section of the Pit River drainage, primarily the Fall River and Hat Creek subdrainages. Habitat requirements are cool, clear, spring-fed streams that include volcanic cobble and boulders (USF&WS, 1998). This species and it's habitat does not occur within the proposed project area. This species is dropped from further consideration. Vernal Pool Fairy Shrimp The vernal pool fairy shrimp is found in vernal pools from Mt. Shasta south to Riverside County. The life cycle of this crustacean is uniquely adapted to temporary ponds and springs. Fairy shrimp eggs are protected form heat and dessication by a tough outer covering. As soon as the eggs are immersed in water reaching 10 degrees C, the eggs hatch. The newly-hatched shrimp eat, grow, reproduce and lay eggs before the ephemeral pools disappear, often in as little as two weeks. Historically, they were widespread, but their populations are now in decline due to the loss of habitat as a result of agriculture and urban development. Though the proposed project lies within the range of this species, there is no suitable habitat. They have therefore been dropped from futher consideration. Vernal Pool Tadpole Shrimp The life history of the vernal pool tadpole shrimp is linked to the seasonal cycle of vernal pools. After winter rains fill pools, the population is reestablished from cysta that lie dormant in the dry pool

9 sediments. The vernal pool tadpole shrimp is known from 18 populations ranging from east of Redding in Shasta County south to Merced County. There are no known populations or habitat within the proposed project area. This species is dropped from further consideration. Sensitive Species A. No Effect Determination. The proposed project will have no effect on the Forest Service sensitive species listed below because suitable habitat for these. species does not exist in the analysis area, or the proposed project lies outside of the range of the species: Hardhead minnow (Mylopharodon conocephalus) Klamath Mtn. Province steelhead ( Oncorhynchus nzvkiss) Upper Klamath/Trinity chinook spring-run (Oncorhynchus tshawvtscha) Upper Trinity River chinook fall-run (Oncorhvnchus tshawytscha) California floater (An.odonta tali/brniensis) Nugget pebblesnail (Flunzinicola seininalis) Scalloped Juga (Juga occata) Montane peaclam (Psidium ultramontanuna) Hardhead Minnow Hardhead are widely distributed in low-to-mid elevation streams in the main Sacramento-San Joaquin River drainages. They are found in the mainstem Sacramento River and it's tributaries to about 1500 m in elevation. As this species and it's habitat does not occur within the proposed project area, this species is dropped from further consideration. Klamath Mtn. Province Steelhead This includes coastal rainbow trout from the Elk River in Oregon through the Klamath and Trinity Rivers. These fish have two distinct spawning runs; one in the winter and another in the summer. The presence of half pounders is charactoristic of this group. As this fish does not occur within the project area, it has been dropped from further consideration. Upper Klamath/Trinity Chinook Spring-Run This run of Chinook salmon is indigenous to the Klamath and Trinity River drainage. This river system once supported large runs of these fish, but the stock was depleted by the turn of the 20 th century as a result of hydraulic mining and in-river commercial fishing. Spring-run Chinook in Klamath-Trinity system are now on the verge of disappearing. This stock of Chinook salmon does not occur within the proposed project are and was dropped from further consideration..

10 Upper Trinity River Chinook Fall-Run C The status of wild fish in the Trinity River is hard to determine because of the millions of hatchery fish that have been released over the years, however the the number of these salmon are but a small fraction of the historic total. Like salmon throughout California their populations have declined dramatically. This fish is indemic to the Klamath-Trinity River drainage and does not occur within the proposed project area. It has therefore been dropped from further consideration. California Floater The California floater is a mussel that lives in shallow areas of clean, clear lakes, ponds and large rivers. They prefer lower elevations and a soft, silty substrate in which to bur r ow. Their life cycle includes a parasitic larval stage, during which it is dependent on host fish for food and dispersal. The decline of the native host fish species, as well as other factors, has been identified as a likely cause of their decline (Frest and Johannes, 1995). Though the proposed project area is within the range of this species, there is no suitable habitat. This species was therefore dropped from futher consideration. Nugget Pebblesnail F. seminalis is a rare snail that preferes cool, clear, flowing water and gravel-cobble substrate. It is typically found in larger creeks and rivers, but is also known to occur on soft, mud substrates in large springs. This species occurs in the Pit and McCloud River basins, and is currently known from only 2 sites on the Shasta-Trinit y National Forest (Furnish and Monthey 1998). This species has never been found in Trout Creek and has therefore been dropped from further consideration. Scalloped Juga This rather rare Sacramento River endemic used to be widespread in the lower Sacramento River, but is now believed to be extirpated (Frest and Johannes, 1995). It is a large river form found generally under loose but stable boulders and cobbles in cold swift water. The species survives at a few sites in the Pit River. This species' present range is outside, the proposed project area. There is no suitable habitat cur r ently present, although the project area may lie within it's former range. This species is therefore dropped from further consideration. Montane Peaclam This species occurs within portions of the Pit River system and it's tributaries, and in the Klamath River system. This clam generally inhabits larger permanent lakes and rivers. It is found in spring-fed areas often on gravel substrate, generally in high diversity mollusk communities. A survey by Frest and Johannes (1995) yielded several individuals in the upper Sacramento River. Though this species occurs within the range of the proposed project area, there is no suitable habitat. This spcies is therefore dropped from futher consideration.

11 B. May Effect'Individuals, but is Not Likely to Adversely Affect the Species Determination. For species listed below, the proposed project may affect individuals. Implementing the proposed project is not likely to adversely affect the species nor result in a trend towards federal listing or create a loss of viability within the planning area of the Shasta-Trinity National Forest, however. In the absense of rangewide viability assessment, this determination is based on local knowledge of the species and professional judgement. McCloud River redband trout (Oncorhynchus mykiss) McCloud River Redband Trout The McCloud river redband trout is native to the upper McCloud river drainage (Siskiyou county). They have a long and clouded taxonomic history, confused by the introduction of nonnative strains of rainbow trout into the system and by past natural connections to the Sacramento River system (Moyle 2002). A conservation agreement was signed in 1998 that guides the management effort of this species. Pesent habitat condition within the proposed project area is extremely poor. Channel downcutting, lateral scour, and the lack of riparian vegetation have resulted in habitat simplification and limited opportunities for habitat improvement. Presently, there are few redband trout found within the proposed project area.. The restoration of the stream to the historic channel would result in opportunities to establish riparian vegetation and improve trout habitat condition. In the long-term there would be a significant increase in the amount of high quality habitat available for redband trout. The short-term effects could result in incidental take of some individuals, however. This potential adversity could be reduced by implementing a fish rescue and relocation effort. This project would lead to an overall improvement in the condition of the redband trout within Trout Creek. Vi. EFFECTS OF THE PROPOSED PROJECT Direct and Indirect Effects Because the project does not lie within the range or include disturbance to suitable habitat for the Central Valley steelhead, coho salmon, delta smelt, winter-run chinook salmon, Shasta crayfish, vernal pool fairy shrimp, vernal pool tadpole shrimp, and Central Valley spring-run Chinook, there are no known direct or indirect effects to the species or habitat of any federally listed threatened or endangered species on the Shasta-Trinity National Forest. Because the project does not include disturbance to suitable habitat for upper Klamath/Trinity spring-run Chinook, upper Trinity River fall-run Chinook, Klamath Mts. Province steelhead, hardhead minnow, California floater, scalloped juga, nugget pebblesnail, or montane peaclam, there are no known direct or indirect effects to the habitats of these Shasta-Trinity National Forest sensitive species. The proposed project may create a short-term adverse affect to individual redband trout and their habitat, but the long-term benefits far exceed any potential adverse effects. The proposed project has the

12 potential to increase the amount of high quality trout habitat as well as increasing the total number of redband trout within Trout Creek. VII. DETERMINATION Based on the above analysis of the proposed Trout Creek Restoration Project it is my determination that: Threatened and Endangered Species Implementation of the project has no effect on Central Valley steelhead, coho salmon, delta smelt, winter-run Chinook salmon, Shasta crayfish, vernal pool fairy shrimp, vernal pool tadpole shrimp, and Central Valley spring-run Chinook salmon. This determination is based on: 1. The proposed project lies outside the current range of these species and/or, 2. There is no suitable habitat for these species. Sensitive Species Implementation of the project will not adversely affect the upper Klamath/Trinity spring-run Chinook, upper Trinity River fall-run Chinook, Klamath Mts. Province steelhead, hardhead minow, California floater, scalloped juga, nugget pebblesnail, or montane peaclam. Implementation of the proposed project may affect individuals of the McCloud River redband trout, but is not likely to adversely affect the species nor result in a trend towards federal listing or loss of viability within the planning area of the Shasta-Trinity National Forest. This determination is based on: I. Suitable habitat for the upper Klamath/Trinity spring-run Chinook, upper Trinity River fall-run Chinook, Klamath Mts. Province steelhead, hardhead minnow, California floater, nugget pebblesnail, scalloped juga or montane peaclam is not present in the proposed project area. 2. This project is in compliance with section X. B. Maintain and Enhance Habitat, as directed by the Conservation Agreement for the Upper McCloud River Redband Trout, Improvement to the overall habitat condition for redband trout will occur upon project implementation.

13 OIII. MANAGEMENT REQUIREMENTS The following mitigation measures are applicable to the proposed action and will be implemented at the project stage to ensure compliance with all directives and reduce or neutralize possible effects on the McCloud River redband trout: Project implementation, layout and designation will be reviewed and monitored on-site by members of the ID Team to ensure all activities are implemented as intended. Best Management Practices as listed in Appendix E of the Forest LRMP will be implemented. A series of fish rescue efforts, conducted by forest fisheries biologists, will occur during project implementation. All redband trout will be relocated to the unaffected perennial stream reaches above the project area. All non-native fish, e.g. brown trout will be removed from the creek during the rescue process. C]

14 References Frest, T.J. and Johannes, E.J Freshwater Mollusks of the Upper Sacramento River and Tributaries with Particular Reference to the Cantara Spill yearly report to Calif Dept of Fish and Game. Deixis Consultants, Seattle, Washington. Frest, T.J. and Johannes, E.J Field Guide to Survey and Manage Freshwater Mollusk Species. Prepared for USDI, Bureau of Land Management, USDI, Fish and Wildlife Service, and USDA, Forest Service. Furnish, J.L. and Monthey, R.W Management Recommendation for Nugget Pebblesnail (Fluminicola seminalis), a ROD Mollusk Species associated with Sacramento River habitats. Prepared for USDA, Forest Service, and USDI, Bureau of Land Management. Moyle, P.B Inland Fishes of California. University of California Press. USDA Forest Service Forest Service Manual Chapter Threatened, Endangered, and Sensitive Plants and Animals. USDA Forest Service, Washington, DC. USDA. Forest Service Shasta-Trinity National Forest Environmental Impact Statement Land and Resource Management Plan. Redding, CA. USDA/USDI Final Supplemental Environmental Impact Statement on Management of Habitat for Late-Successional and Old-Growth Forest Related Species Within the Range of th Northern Spotted Owl. Vol. I & II. USDA/USDI Record of Decision and Standards and Guidelines for Amendments to the Survey and Manage, Protection Buffer, and other Mitagation Measures Standards and Guidelines. USDI Fish and Wildlife Service Recover y Plan for the Shasta Crayfish (Pacifastacus _fortes) August 2S, 1998