ASSESSMENT OF THE EFFECTS OF INTERIM PROJECT OPERATIONS ON BULL TROUT AND BALD EAGLE

Baker River Hydroelectric Project (FERC No. 2150) Washington ASSESSMENT OF THE EFFECTS OF INTERIM PROJECT OPERATIONS ON BULL TROUT AND BALD EAGLE ADDENDUM TO: BIOLOGICAL ASSESSMENT OF PROPOSED INTERIM CONSERVATION MEASURES FOR PUGET SOUND CHINOOK SALMON PENDING RELICENSING Unpublished Work, Copyright 2002, Puget Sound Energy, Inc. Puget Sound Energy, Inc. December 2002

CONTENTS 1. INTRODUCTION... 1-1 2. PROJECT DESCRIPTION... 2-1 2.1 LOWER BAKER DEVELOPMENT... 2-1 2.2 UPPER BAKER DEVELOPMENT... 2-3 2.3 BAKER PROJECT FISH FACILITIES... 2-3 3. REGULATORY PROCESS ISSUES... 3-1 3-1 ACTION AREA... 3-1 3-2 SPECIES ADDRESSED BY THIS BIOLOGICAL ASSESSMENT... 3-1 3.2.1 Bull Trout (Salvelinus confluentus)... 3-2 3.2.2 Dolly Varden (Salvelinus malma)... 3-6 3.2.3 Bald Eagle (Haliaeetus leucocephalus)... 3-6 3.3 ACTIVITIES TO BE COVERED BY THE BA... 3-8 3.3.1 Storage and Release of Water for Power Generation and Flood Control... 3-8 3.3.2 Flow Management for Aquatic Resource Protection... 3-10 3.3.3 Fish Passage... 3-10 3.3.4 Fish Propagation and Release... 3-10 3.3.5 Routine Operation and Maintenance... 3-11 4. EXISTING AND PROPOSED INTERIM CONSERVATION MEASURES... 4-1 4.1 PROPOSED LICENSE AMENDMENT... 4-1 4.2 RESEARCH AND MONITORING ACTIVITIES... 4-6 5. ENVIRONMENTAL ANALYSES... 5-1 1145.15.Baker-Bull Trout BA.120502 ii Bull Trout and Bald Eagle

5.1 BULL TROUT... 5-1 5.1.1 Mainstem Skagit River Conditions... 5-1 5.1.2 Baker River to Skagit River Habitat Access... 5-3 5.1.3 Reservoir and Tributary Conditions... 5-10 5.1.4 Water Quality... 5-17 5.1.5 Ecosystem Functions... 5-22 5.2 BALD EAGLE... 5-24 5.2.1 Nesting and Roosting... 5-25 5.2.2 Foraging... 5-26 6. INTERRELATED, INTERDEPENDENT AND INDIRECT EFFECTS... 6-1 6.1 SKAGIT COUNTY FLOODPLAIN MANAGEMENT... 6-1 6.2 U.S. ARMY CORPS OF ENGINEERS FLOOD CONTROL... 6-1 6.3 U.S. ARMY CORPS OF ENGINEERS ECOSYSTEM RESTORATION STUDIES... 6-2 6.4 SKAGIT COUNTY STRATEGIC PLAN FOR PROTECTING WILD SALMONIDS... 6-2 6.5 HATCHERY AND HARVEST PRACTICES... 6-4 6.6 FUTURE LICENSING OF THE BAKER PROJECT... 6-5 6.7 SKAGIT RIVER HYDROELECTRIC PROJECT (FERC NO. 553)... 6-6 6.8 ANALYSIS OF EFFECTS ON LISTED SPECIES... 6-7 7. DETERMINATION OF EFFECT AND TAKE ANALYSIS... 7-1 7.1 BULL TROUT... 7-2 7.2 BALD EAGLE... 7-6 8. REFERENCES CITED... 8-1 1145.15.Baker-Bull Trout BA.120502 iii Bull Trout and Bald Eagle

LIST OF FIGURES Figure 1-1: Baker River Hydroelectric Project, Concrete, Washington...1-2 Figure 2-1: Schematic of Lower Baker Development...2-2 Figure 2-2: Schematic of Upper Baker Development...2-4 Figure 5-1: Guide-net modifications and the number of juvenile salmonids using the downstream migrant facility at Baker Lake, Washington, 1987 through 1999....5-7 Figure 5-2: Estimated passage system effectiveness based on hydroacoustics monitoring at Baker Lake, Washington, from 1988 through 1995...5-8 Figure 5-3: Adult sockeye returns at Baker River, Washington, 1916 through 1996...5-9 Figure 5-4: Baker Lake pool elevations recorded every two weeks during the period 1979 through 2002; 90 percent, 50 percent and 10 percent exceedance levels calculated using period 8/79 through 7/99 to avoid extreme 2001 pool fluctuations associated with major project maintenance...5-13 Figure 5-5: Lake Shannon pool elevations recorded every two weeks during the period 1979 through 2002; 90 percent, 50 percent and 10 percent exceedance levels calculated using period 8/79 through 7/99 to avoid extreme 2001 pool fluctuations associated with major project maintenance....5-14 Figure 5-6: Water and air temperatures recorded in 15-minute intervals in middle Skagit River between River Mile 31.7 and River Mile 36.5 during late August and September 2002. Air temperatures recorded within dense-canopied riparian area and reflects microclimate influences...5-21 Figure 7-1: Summary diagnostics matrix of effects of the proposed interim conservation measures for the Baker River Hydroelectric Project (FERC No. 2150) on bull trout (Salvelinus confluentus) pending Federal Energy Regulatory Commission Baker Project relicensing....7-5 Figure 7-2: Summary diagnostics matrix of effects of the proposed interim conservation measures for the Baker River Hydroelectric Project (FERC No. 2150) on bald eagle (Haliaeetus leucocephalus) pending Federal Energy Regulatory Commission Baker Project relicensing....7-7 1145.15.Baker-Bull Trout BA.120502 iv Bull Trout and Bald Eagle

TABLES Table 3-1 Number of Dolly Varden/bull trout (native char) trapped and hauled above the Baker Project since 1994. Annual counts of native char transported above the Baker Project were not recorded prior to June 1994 (A. Aspelund, PSE, pers. comm. 2002)...3-5 Table 5-1 Number of native char collected each month at the adult fish trap and released above Baker Lake (1995-2002)...5-4 Table 5-2 Number of juvenile native char captured at downstream fish passage facilities at the in the period 1994-2002. Native char were recorded in the other species category prior to 1994 and annual counts are not available...5-6 Table 5-3 Theoretical estimate of downstream passage efficiency and fate of native char moving downstream at the...5-12 1145.15.Baker-Bull Trout BA.120502 v Bull Trout and Bald Eagle

1. INTRODUCTION The, FERC No. 2150 (the "Baker Project"), is owned and operated by Puget Sound Energy, Inc. ("PSE"). The Baker Project consists of two hydroelectric generating developments; both located on the Baker River, in Washington State. Construction of the Lower Baker Development, including the Lower Baker Dam at River Mile (RM) 1.2, was completed in 1925 prior to the enactment of the Federal Power Act. In 1927, the Federal Power Commission (now known as the Federal Energy Regulatory Commission or "FERC") issued a license to Puget Sound Power & Light Company (now known as PSE) to operate the Lower Baker Development. The Federal Power Commission subsequently issued a License in 1956 to construct the Upper Baker Development. The License combined the operations of both developments into a single federal license for the Baker Project (Figure 1-1). Construction of the Upper Baker Development, including the Upper Baker Dam at River Mile (RM 9.2), was completed in 1959. The Baker Project license expires in 2006. PSE filed a notice of intent to relicense the Project in April 2001, and plans to file an application to relicense the Project on or before April 30, 2004. In advance of that filing, PSE (as the prospective license applicant) initiated informal consultation as the non-federal designee under Section 7 of the Endangered Species Act (ESA) with respect to relicensing of the Project. Under Section 7, "a federal agency shall consult with the Secretary [of Commerce or Interior, as appropriate] on any prospective agency action at the request of, and in cooperation with, the prospective permit or license applicant if the applicant has reason to believe that an endangered species or threatened species may be present in the area affected by his project and that implementation of such action will likely affect such species" 16 USC 1536(a)(3). There are several listed species in the Project Area, including chinook salmon (Oncorhynchus tshawytscha) (63 FR 11482) and bull trout (Salvelinus confluentus) (64 FR 58909) listed as threatened, and bald eagle (Haliaeetus leucocephalus) listed as threatened, but recently proposed for delisting (64 FR 36454). Operation of the Baker Project affects flows in the lower 1.2 miles of the Baker River, affects flows in the mainstem Skagit River downstream of RM 56.5 and affects pool level fluctuations in the two reservoirs. The mainstem Skagit River is also affected by operation of Seattle City Light s Skagit River Hydroelectric Project (FERC No. 553) (the Skagit Project ) located approximately 40 miles upstream of the Baker River's confluence with the Skagit River. Both the Baker Project and the Skagit Project are typically operated as load-following plants. Baker typically operates once or twice a day, usually during mornings (i.e., 0600 to 1000) and evenings (i.e., 1700 to 2100). These periods of operation vary daily, weekly and seasonally in response to power demands and power value. For instance, electrical demand is generally higher Monday through Friday and in response, the Project may not operate during the weekend. Daily peaking operations may cause flows in the Lower Baker River to fluctuate up to 4,200 cfs. 1145.15.Baker-Bull Trout BA.120502 1-1 Bull Trout and Bald Eagle

Figure 1-1: Baker River Hydroelectric Project, Concrete, Washington 1145.15.Baker-Bull Trout BA.120502 1-2 Bull Trout and Bald Eagle

In the late fall 2000, NMFS and USFWS became concerned that generation by the Baker Project and Skagit Project supplemented flows in the Skagit River, causing fish to spawn at higher elevations, and that subsequently when water became scarce in the 2000-2001 drought, salmon redds were exposed for extended periods, resulting in egg desiccation. As an aspect of PSE's plans to pursue early Section 7 consultation on its proposed new license for the Baker Project, PSE undertook additional discussions to address matters of interest to the Services pending relicensing. First, representatives of PSE and the Services, working with the Baker Committee, developed a proposed arrangement for near-term Baker Project operations to help mitigate the salmon production impact of the low instream flows resulting from the previous winter's unusually dry natural weather conditions. PSE, in consultation with the tribes and resource agencies, operated the Baker Project reservoirs to conserve and use water for fish protection during the winter months. To help minimize egg desiccation pending fry emergence, PSE, in consultation with resource agencies and tribes, operated the Baker Project to generate strategic "pulses" of water, pulsing flows to bathe the redds to help avoid or reduce egg desiccation during the drought. This allowed the Baker Project to provide up to a "periodic" incubation base flow of 7,600 cfs for long enough each day to keep eggs wet and unfrozen, when the natural Skagit River flow was significantly lower, and when continuous generation would have caused the Baker Project to run out of water. Following emergence, project generation and a maintenance outage were, again in consultation with resource agencies and tribes, completed in the manner deemed most advantageous to chinook and other fish resources under the circumstances. Following on those efforts, representatives of PSE, FERC and the Services have been working to develop a plan of operations for the Project pending relicensing on a going-forward basis, in coordination with or taking account of the Skagit Project operations, in a manner that optimizes, to the extent possible, the power benefits of Skagit system hydroelectric operations while at the same time minimizing any effects of PSE's (and Seattle City Light's operations) on listed species. While the 2000-2001 drought figured prominently in these discussions, they have also considered operational scenarios to address more "normal" and "wet" weather conditions, and particularly how the project's flood control capabilities could be brought to bear to help protect and recover Puget Sound chinook salmon and bull trout. The ESA serves to identify and provide mechanisms to protect species of plants and animals, which are considered to be threatened with or in danger of extinction. The law is administered by the U.S. Fish and Wildlife Service (USFWS), a subunit of the Department of Interior, for terrestrial plants, animals and resident fish, and by the National Marine Fisheries Service (NMFS), a subunit of the Department of Commerce, for marine animals and anadromous fish. These two agencies are often collectively referred to as "the Services." Listed species are present in the Project area. As an aspect of relicensing, the federal agency responsible for licensing the Baker Project, FERC, will be required to document in a biological assessment the degree to which the proposed action may adversely affect any threatened or endangered species found in the proposed project area or destroy or adversely modify designated critical habitat. The agency makes a determination of the biological effects of the action. In response, the Services will either concur with the assessment or prepare a Biological Opinion (BO), which first determines whether the adverse effects of an action would jeopardize the continued existence of any species or destroy or adversely modify designated critical habitat of the species and, if so, whether the 1145.15.Baker-Bull Trout BA.120502 1-3 Bull Trout and Bald Eagle

action agency could avoid causing jeopardy or such destruction or adverse modification of critical habitat by pursuing reasonable and prudent alternatives. Thereafter (assuming the action or reasonable prudent alternatives to the action will not jeopardize the continued existence of the species), the Services identify reasonable and prudent measures (RPM) to minimize the impact of incidental taking of the species, and describes the terms and conditions that must be complied with by the Federal agency or applicant, or both, to implement the measures. By letter dated March 5, 2001, the FERC authorized PSE to act as its non-federal designee in consultation with the Services, subject to limitations described in the Commission s order. As the non-federal designee, PSE recognized the Commission's objectives of compliance with the ESA with the goal of ensuring protection and contributing to recovery of listed species pending its relicensing decision and the Services' authorization for incidental take associated with such operations under Section 7 of the ESA for such interim period. In developing the interim protection plan, PSE was also mindful of the Commission's directive that Licensees assure that energy supplies are maintained, where possible increased, and safeguarded. E.g., Removing Obstacles to Increased Electric Generation and Natural Gas Supply in the Western United States, (94 FERC 61,272) and Extraordinary Expenditures Necessary to Safeguard National Energy Supplies, Docket No. PL01-6- 000 (96 FERC 61,299). On June 13, 2002, after consultation with representatives of the FERC and the Services, PSE filed a draft biological assessment evaluating the potential effects of continued project operation on chinook salmon and an amendment application that proposes measures to conserve chinook salmon. The interim protection plan contained in the draft biological assessment is intended to identify interim measures to minimize impacts to Puget Sound chinook salmon pending relicensing of the Baker Project. Commission staff issued a public notice for the amendment application on August 13, 2002, and requested consultation with NMFS. By letter dated September 23, 2002, the FERC requested that PSE pursue informal consultation with the USFWS and prepare a draft biological assessment for bull trout and bald eagle. The objective of the additional consultation and development of a supporting BA is to evaluate the potential effect of conservation measures identified in the chinook BA on bull trout and bald eagle including any proposed changes to operations designed to benefit chinook salmon. Baseline information about the Baker Project and its operations are presented in Section 2. The status of bull trout and bald eagle and habitats affected by the Baker Project and regulatory process issues are described in Section 3, while Section 4 contains an abridged description of the proposed interim conservation measures. This document is intended to supplement the draft biological assessment submitted to the NMFS; and where practical, detailed information presented in the chinook biological assessment is summarized rather repeated. The environmental analyses, including a description of the environmental resources in the project area and the effects of proposed interim measures on those resources, are described in Section 5. Section 6 contains analyses of Interrelated, Interdependent and Cumulative Effects specific to project effects on bull trout and bald eagle. A summary of the Effects Analyses is contained in Section 7. In addition to analyses and discussions conducted as part of Section 7 pre-filing consultations, a number of environmental studies are being conducted as part of the FERC relicensing effort. These studies will allow a more complete understanding of the status and needs of bull trout and chinook salmon in the 1145.15.Baker-Bull Trout BA.120502 1-4 Bull Trout and Bald Eagle

Baker and Skagit Rivers to inform the discussions and decisions regarding relicensing of the Baker Project, including further ESA consultation regarding terms and conditions that should be included in the new license. By federal register notice 64 FR 36454, the USFWS has found that there is substantial scientific and commercial information indicating that a change in the status of the listed bald eagle may be warranted. Should bald eagles be delisted as a threatened species under the ESA, this BA may be modified to delete discussion of bald eagles. 1145.15.Baker-Bull Trout BA.120502 1-5 Bull Trout and Bald Eagle

2. PROJECT DESCRIPTION PSE s Baker Project is located in the Baker River Basin on the west side of the Cascade Mountains in Washington State. The Baker River, the second largest tributary to the Skagit River, originates in the glacial fields of Mount Baker and Mount Shuksan and has an average annual flow of 2,667 cubic feet per second (cfs) (USGS Gage No. 12193500, period of record 1911-14, 1944-2000). The basin, which is largely uninhabited, is located within a very steep, mountainous region on the west side of the Cascade Mountains. The Baker Project consists of two major hydroelectric developments, Lower and Upper Baker. 2.1 LOWER BAKER DEVELOPMENT The Lower Baker Development consists of the Lower Baker Dam, a powerhouse, reservoir and associated facilities. Lower Baker Dam is located on the Baker River approximately 1.2-miles north of the confluence of the Baker and Skagit Rivers. The powerhouse contains a single generating unit (Unit 3). The single turbine was replaced in the spring of 2001 and the new unit has a maximum machine flow of approximately 4,700-cfs and is capable of producing 77 megawatts (MW) of electricity. However, the maximum generating flow is currently limited to 4,200-cfs due to limitations of the transformer. Unit 3 efficiently operates at flows between 3,700 cfs to 4,100 cfs at a net head of 253 feet, and has a minimum machine flow of approximately 3,200 cfs (Figure 2-1). Under current operations, water in the lower Baker River passes through the single power-generating unit at Lower Baker Dam, through a 24-inch bypass pipe (80 cfs), leakage through pressure relief holes in dam abutments, or is spilled through the Lower Baker Dam over the spillway crest at elevation 425-feet. When Lower Baker Unit 3 shuts down, an 80-cfs flow is continually released below Lower Baker through the 24-inch bypass valve to allow operation of the adult trap-and-haul facility. During periods of peak sockeye adult migration (i.e., late June through July), PSE has typically generated for 4 hours beginning at daylight into the Lower Baker River to provide additional attraction for adult fish staging at the confluence of the Baker and Skagit Rivers. Lake Shannon, the reservoir formed by Lower Baker Dam, is approximately seven miles long and covers an area of about 2,218 acres at normal full pool (elevation 438.6 feet). Approximately 159,465 acre-feet of water are stored in Lake Shannon at full pool, including about 122,565 acre-feet of active storage above the minimum generation level. The top of Lower Baker Dam is at elevation 446.87 feet, and water is released through the turbine intake (elevation 350 feet) or through the dam spillway (spillway crest elevation 424.8 feet). Under normal operating conditions, Lake Shannon is held at full pool during the summer months. Minimum reservoir elevations are typically attained from November through March or early April. Lake Shannon can be operated in coordination with Baker Lake to provide flood control protection, but there is no formal agreement governing Lake Shannon operations for storage of winter storm runoff. 1145.15.Baker-Bull Trout BA.120502 2-1 Bull Trout and Bald Eagle

Lower Baker Dam Section View - Not to Scale Turbine eration (cfs) rmal max 1 ak efficiency 1 rmal min 1 ergency min 1 W 2 Unit #3 (new) 4,200 2 3,800 3,200 N/A 3 71.36 gate capacity 40 kcfs at elev. 438.6 top of dam elev. 446.87 438.6 normal full pool 424.8 spillway crest 390 avg. minimum pool 28,549 acre ft. active pool 122,565 acre ft. aries with reservoir pool elev. urbine capacity of 4,700 cfs presently ited by transformer capacity ata not available or untested intake top elev. 350 unusable storage 36,900 acre ft. 370 minimum generating pool 22 dia. concrete-lined penstock intake invert elev. 330 Full pool surface area = 2,218 acres Full pool volume = 159,465 acre ft. Required flood control volume = 0 Reservoir length = 7 miles powerhouse unit #3 ertical Francis Two intakes 20 H x 12 W, transition to single 22 dia. penstock, bifurcates to (2) 16 dia. near pwrhse 23 spill gates, each 14 H x 9.5 W, top of gates 438.8, 5 of 13 automatic are remote-controlled, 10 manual Rated net head = 243 24 bypass Darling valve 80 cfs 16 butterfly valve dam base elev. 162 Constructed 1924-11/25 with 4 Francis units 33 elev. added 1927, total height 285 Concrete gravity arch dam 550 long Added unit #3 1960, all destroyed 1965 by landslide, rebuilt 09/68 with unit #3 only Figure 2-1: Schematic of Lower Baker Development 1145.15.Baker-Bull Trout BA.120502 2-2 Bull Trout and Bald Eagle

2.2 UPPER BAKER DEVELOPMENT The Upper Baker Development consists of the Upper Baker Dam, a powerhouse, reservoir and associated facilities. The Upper Baker powerhouse contains two generating units (Units 1 and 2) with a collective capacity of about 92.5 MW and a collective maximum machine flow of approximately 5,050 cfs. Baker Lake, the reservoir formed by Upper Baker Dam, is approximately nine miles long and covers an area of about 4,800 acres at normal full pool (elevation 724.0 feet). Roughly 285,472 acre-feet of water are stored in Baker Lake at full pool, of which approximately 184,796 acre-feet is active storage above the minimum generating pool (Figure 2-2). The top of Upper Baker Dam is at elevation 732 feet and water is released through the turbine intakes (elevation 654 feet) or through the spillway (spillway crest elevation 694 feet). Under normal operating conditions, Baker Lake is held near full pool during the summer months. Minimum reservoir elevations are typically attained from November through March or early April. PSE's license obligates PSE to operate the Upper Baker Development to provide the United States Army Corps of Engineers (the "Corps") with 16,000 acre-feet of flood control storage between November 1 and March 1. In addition, PSE is obligated to provide up to 84,000 acre-feet of additional flood control storage if requested by the Corps (for a total of up to 100,000 acre-feet of flood control storage). Under the current agreement between PSE and the Corps, PSE must maintain Baker Lake elevations at or below 720.75 by November 1 (to provide a total of 16,000 acre feet of flood control storage at the Upper Baker Development) and to elevation 707.8 feet or lower under normal operating conditions from November 15 to March 1 (to provide a total of 74,000 acre-feet of flood control storage at the Upper Baker Development). 2.3 BAKER PROJECT FISH FACILITIES The upstream and downstream fish passage facilities at the Baker Project provide the opportunity for movement of anadromous fish between the Baker River above and below (and from within) the Baker Project. Anadromous fish leave the Baker River, travel out the Skagit River to Puget Sound and the ocean, and return again via the Skagit River to the Baker River. Fish passage at the Baker Project consists of three separate facilities: 1) the barrier dam and adult fish trap; 2) Lower Baker downstream fish passage; and 3) Upper Baker downstream fish passage. An upstream trap and haul fish passage facility (i.e., barrier dam, fish trap, holding ponds and fish lift) has operated at the Baker Project since 1926 near RM 0.6. The small barrier dam blocks adult fish from continuing upstream and helps guide them into a trapping facility, where they are lifted into a tank truck for transport to different locations depending on the species. Between 1926 and 1995, an average of 9,400 adult salmon and steelhead have been counted at the Baker River trap on an annual basis. Fish are collected at the barrier dam using an adult trap where they pass through the entrance vestibule into a series of three holding ponds. Adults are sorted and evaluated in the uppermost pond, which contains a brail that can be mechanically raised or lowered, and moved into the hopper. From the hopper, fish are transferred to the transport truck for release. The bottom of the hopper is designed to seat securely with 1145.15.Baker-Bull Trout BA.120502 2-3 Bull Trout and Bald Eagle

Upper Baker Dam Section View - Not to Scale Turbine eration (cfs) Unit 1 Unit 2 rmal max 1 ak efficiency 1 rmal min 1 ergency min 1 W 2,550 2,250 1,950 52.40 2,500 1,900 1,300 800 38.30 gate capacity 48 kcfs at elev. 724 top of dam elev. 732 724 normal full pool 707.8 flood control elev. (11/15-03/01) 694 spillway crest 126,949 acre ft. active pool 184,796 acre ft. aries with reservoir pool elev. 674 minimum generating pool intake top elev. 654 unusable storage 100,676 acre ft. (2) 13.5 dia. steel penstocks intake invert elev. 634 Full pool surface area = 4,985 acres Full pool volume = 285,472 acre ft. FERC-required flood control volume = 16,000 acre ft. (720.75, 11/01-03/01) USACE/PSE agreed flood control volume = 58,000 acre ft. (707.8, 11/15-03/01) Reservoir length = 9 miles Project Storage (acre ft.) Upper Lower Combined powerhouse Francis units #1 & 2 tailwater elev. 439 dam base elev. 420 Total active Total above spillways 184,796 126,949 122,565 28,549 Two intake gates 20 H x 16 W, transition to two 13.5 dia. steel penstocks Three tainter spill gates, each 30 H x 25 W, top of gates 724, spillway crest 694.0 Net hydraulic head = 297, rated net head = 285 Constructed 06/56-10/59 with 2 Francis units Concrete gravity dam 1200 long, 312 high 12 roadway at elev. 732 Figure 2-2: Schematic of Upper Baker Development 307,361 155,498 1145.15.Baker-Bull Trout BA.120502 2-4 Bull Trout and Bald Eagle

the top of the transport truck for a water-to-water transfer. The trap is typically operated year-around, except for a brief maintenance/repair period in May or June. Downstream migrating fish are collected at Lower and Upper Baker using a barrier net guidance system, attraction barge and fish trap/sampling facility. Juvenile fish moving downstream through the reservoir encounter the barrier net and move towards the attraction barge, also known as the gulper. Pumps mounted on the attraction barge create a flow net attracting migrating fish towards the barge entrance. The mouth of the Upper Baker barge entrance is 12 feet wide by 9 feet high. Total flow entering the gulper barge is 70,000 gallons per minute (gpm). There are two primary pumpback pumps each rated at 35,000 gpm at 5 feet head and are driven with a 75 hp motor. Wooden louvers, with approximately 1/2- to 1-inch clear spacing (depending on location), are on the floor and sidewalls throughout the 42-foot length. The floor of the barge entrance is initially flat but gradually slopes up over a distance of 42 feet. At the downstream end, the floor gradually narrows to a 3-foot wide chute. Excess water drawn by the pumps is passed through the louvers and discharged on either side of the barge. Approximately 6,000 gpm enter the chute with up to 4,500 gpm pumped back to the reservoir. The remaining 1,500 gpm transport the fish transported to the holding and transportation barge. The Lower Baker Gulper is similar to the Upper Baker facility though smaller in scale (40,000 gpm). The gulpers are normally put in operation in March and run through end of July. The barrier guide net systems at both Lower and Upper Baker are constructed of 1/4-inch, square mesh netting and are designed to extend completely across the forebay. The net is anchored to the bottom of the reservoirs with weights and an airline from the collection barge is attached to a flexible pipeline at the top of the nets acting as a corkline to maintain flotation and form a seal of the net to the surface. During conditions of impending spill, the flexible pipeline is flooded, submerging the top section of the nets to reduce drag during spill events. After the spill event, the pipeline is evacuated of water refloating the nets to restore the barrier provided by the guide net system. Downstream migrants are captured, sampled for biological information, transferred to a tank trailer and trucked to the mouth of the Baker River where they are released. During the 5-year period 1995 to 1999, an average of 200,247 smolt-sized juvenile salmonids per year have been transported downstream from the Upper and Lower Baker Developments. Some juvenile anadromous salmonids may also pass over the spillways or through the turbines. During the 1950s, the results of research indicated that sockeye smolts passing over the spillway at Lower Baker sustained a survival rate of 46 percent, while juvenile salmon passing through the turbines experienced a 66 percent survival rate (Hamilton and Andrew, 1954). Studies have not been conducted to quantify the fish guidance efficiency of the facilities. Salmonid fry are not frequently observed at the trap. Juvenile bypass pipelines exist at both Upper and Lower Baker Developments; however, trap and haul is currently the preferred (and currently necessary) transportation method. Landslides and a spill event at Lower Baker interrupted the connectivity of the bypass pipelines and repairs are difficult due to the location, the topography and the configuration of the canyon through which it transits. Downstream passage facilities were fully operational (i.e., modified barrier nets, attraction barge, fish trap/sampling 1145.15.Baker-Bull Trout BA.120502 2-5 Bull Trout and Bald Eagle

area, fish transport system) at both Upper and Lower Baker during the 2001 and 2002 outmigration seasons. In addition to fish passage facilities, PSE also operates a spawning beach complex to facilitate the reproduction of sockeye salmon (O. nerka) in the Baker River. Surveys conducted by the Washington Department of Fisheries in the 1950s prior to construction of the Upper Baker Dam identified that most sockeye spawned along southern shore of the original Baker Lake utilizing gravel areas with underground flow. Stream spawning sockeye appeared generally limited to Channel Creek, which contained a strong underground flow similar to the lakeshore environments (Quistorff 1992). Construction of the Upper Baker Development raised the level of the original Baker Lake nearly 60 feet and created a nine-mile long reservoir. The spawning beach complex was designed to replace the original Baker Lake sockeye spawning beds inundated by the Upper Baker reservoir. Three spawning beaches are located at the northern end of Baker Lake (Figure 1-1). Spawning beaches 1, 2 and 3 are located together at one facility near Channel Creek (Beach 1 is not functional and has not been used since 1965). Beaches 2 and 3 are used intermittently by the Washington Department of Fish and Wildlife (WDFW) to augment production during years of high returns. The water supply for these facilities originates from a spring and surface water collector. Spawning Beach 4, constructed near Sulphur Creek in 1990, replaced Beaches 1, 2 and 3. A spring located on the north side of Sulphur Creek provides water for Beach 4. Fry are allowed to leave Beach 4 on their own volition, directed into a trap and haul facility and trucked to Baker Lake for release. Baker River sockeye carry the Infectious Haematopoietic Necrosis (IHN) virus. Therefore Beach 4 was divided into four segments to isolate disease outbreaks by segregating the population into smaller groups of fish and preventing water transfer between the sections. Approximately 2.5 cfs is supplied to each beach section (10 cfs total). Fry are tested periodically for IHN at a WDFW laboratory. In the event of an IHN outbreak, effluent from Beach 4 can be diverted through a chlorination/dechlorination system that kills the IHN virus before it enters Sulphur Creek. 1145.15.Baker-Bull Trout BA.120502 2-6 Bull Trout and Bald Eagle

3-1 ACTION AREA 3. REGULATORY PROCESS ISSUES The Baker Project consists of two dams (Lower and Upper Baker Dams), two reservoirs (Lake Shannon and Baker Lake) and limited lands near the dams that are used for Project operational purposes. The Project boundary encompasses approximately 8,100 total acres consisting of 7,203 total acres of reservoir surface area and approximately 910 acres of land. The Action Area for Project operation and maintenance is described as: Lower Baker Dam and associated power production facilities Lake Shannon up to the ordinary high water mark Upper Baker Dam and associated facilities Baker Lake up to the ordinary high water mark upstream and downstream fish passage facilities fish production facilities Lower Baker River between Lower Baker Dam and the Skagit River confluence the Skagit River within the active floodplain downstream of the confluence of the Baker and Skagit rivers (RM 56.5). 3-2 SPECIES ADDRESSED BY THIS BIOLOGICAL ASSESSMENT Coho (O. kisutch) and sockeye (O. nerka) are the dominant salmon stocks in the Baker River system and comprise about 94 percent of total trap return numbers. Chinook, pink (O. gorbuscha), chum (O. keta) salmon and steelhead (O. mykiss), together comprise about 6 percent of average trap returns. During the 6-year period June 1994 through May 2000, an average of 19.5 adult bull trout/dolly Varden (S. malma) per year were hauled above the Baker Project. It is unknown whether the adult char entering the Baker trap originated in the Baker River. This BA is intended to describe an analysis of the effects of the proposed actions identified in the draft biological assessment for chinook salmon on bull trout and bald eagle. The Coastal/Puget Sound Distinct Population Segment (DPS) of bull trout was listed as threatened in November 1999 (64 FR 58910) and is likely present in the middle Skagit River, the Baker River, Baker Project reservoirs and tributaries. Dolly Varden (S. malma) may also be present in the Project area and are under consideration for listing due to similarity of appearance to Coastal/Puget Sound bull trout (66 FR 1628). Both bull 1145.15.Baker-Bull Trout BA.120502 3-1 Bull Trout and Bald Eagle

trout and Dolly Varden are char, classified in the genus Salvelinus, and are administered by the USFWS. References to bull trout, or use of the term native char in this document are assumed to reflect both bull trout and Dolly Varden unless potential differences are specifically identified. The BA also addresses the effects of the interim conservation measures on bald eagle (Haliaeetus leucocephalus) foraging, nesting and winter roosting since the species is known to occur in the Project Area. The bald eagle is proposed for delisting under the ESA, but it currently remains listed as threatened in Washington State. Although pink salmon (O. gorbuscha), and chum salmon (O. keta) and coho salmon (O. kisutch) are not currently listed under the ESA, project effects on these salmon species are analyzed to support the evaluation of project effects on bald eagle foraging. 3.2.1 Bull Trout (Salvelinus confluentus) Bull trout are native to most of the interior and some coastal drainages of the Pacific Northwest (63 FR 31693). Populations of bull trout are found in western Washington, including coastal drainages of the Puget Sound, Straight of Juan de Fuca, Hood Canal, and Olympic Peninsula (64 FR 58910). Bull trout have been recorded from northern California, the Klamath River basin in Oregon, throughout much of interior Oregon, Washington, Idaho, western Montana and British Columbia, Hudson Bay and the St. Mary s River Saskatchewan, but are shrinking in distribution throughout their former range (63 FR 31693). Native char in Puget Sound and coastal streams may express both resident and migratory life history forms (USFWS 1998). Resident bull trout complete their life cycles in freshwater, while some migratory bull trout adopt an anadromous life cycle. Anadromous forms migrate to marine areas in the spring and return in late summer and early fall (Wydoski and Whitney 1979). Native char can spend 2 or 3 years in freshwater before migrating to sea. Little is known about their habits or distribution while in the marine environment. Resident bull trout may express adfluvial and riverine life history forms, sometimes both within one watershed. Adfluvial stocks rear in lakes or reservoirs before returning to tributary streams to spawn, whereas riverine forms spend their entire life cycle in streams. In some river systems that are known through genetic testing to contain both species of char (Dolly Varden and bull trout) and their hybrids, it appears that Dolly Varden mature at a smaller size and exhibit a riverine life history, whereas bull trout are generally adfluvial and larger-bodied (McPhail and Taylor 1995, Baxter et al. 1997; Hagen and Taylor 2001; Taylor et al. 2001). In the East Fork Quinault River on the Olympic Peninsula, the two species both occur in the mainstem, but only Dolly Varden have been found in tributary habitat (Leary and Allendorf 1997). Similarly, both bull trout and Dolly Varden occur in the Skagit River upstream of Ross Lake and the smaller Dolly Varden were noted to be stream residents, whereas bull trout were predominate in the main river and reservoir (McPhail and Taylor 1995). A study in the South Fork Sauk River, which is a tributary to the Skagit downstream of Ross Lake, indicated that it contained only bull trout (Leary and Allendorf 1997). 1145.15.Baker-Bull Trout BA.120502 3-2 Bull Trout and Bald Eagle

Spawning in most native char populations occurs in September and October, though it may occur in August at elevations above 4,000 feet in the Cascades and as late as November in coastal streams (Goetz 1989; Craig 1997). Most anadromous populations spawn only every second year, while resident char may spawn every year (Armstrong and Morrow 1980; USFWS 1998). Spawning sites are characterized by low gradient, uniform flow, and a gravel substrate between (between 0.6 and 5 centimeters in diameter) (Wydoski and Whitney 1979; Fraley and Shepard 1989). Groundwater influence and proximity to cover are also reported as important factors in spawning site selection (Fraley and Shepard 1989). Studies conducted throughout the species range indicate that spawning occurs in water from 0.75 to 2.0 feet deep (Wydoski and Whitney 1979; Fraley and Shepard 1989) and often occurs in reaches fed by streams, or near other sources of cold groundwater (Pratt 1992). Bull trout require a long period of time from egg deposition until emergence. Embryos incubate for approximately 100 to 145 days, and hatch in late winter or early spring (Weaver and White 1985). Rieman and McIntyre (1993) indicate that optimum incubation temperatures are between 2 and 4ºC. The alevins remain in the streambed, absorbing the yolk sac, for an additional 65 to 90 days (Pratt 1992). Emergence from the streambed occurs in late winter/early spring (Pratt 1992). High fine sediment levels in spawning substrates reduce embryo survival, but the extent to which they affect bull trout populations is not entirely known (Rieman and McIntyre 1993). Long over-winter incubation periods for native char embryos and alevins make them particularly susceptible to increases in fine sediments (USFWS 1998). Native char are typically thought of occurring in steeper gradient, upstream reaches than other salmonid species. Adult native char can navigate waterfalls and cascades that impede upstream migration for other species. Rather than exhibiting unusual leaping abilities, bull trout have been observed to seek out channel margins and bypass falls during high flow events or to burrow through logjams to ascend to upstream reaches. Native char can also exhibit a patchy distribution, where they are not found in all tributaries or reaches within a watershed (Watson and Hillman 1997; Baxter 1995). Native char may occur in greater densities in upstream, typically higher gradient reaches, as a result of higher water temperatures in downstream reaches, and possibly an inability to compete effectively against other salmonids (Stolz and Schnell 1991). The WDFW lists the following as the limiting factors for the species: stream temperatures that exceed the normal spawning and incubation temperature range; lack of spawning and rearing habitat; and a high percentage of fine sediment in spawning gravels (WDFW 1998). Because of their close association with the bottom, native char are sensitive to changes in the streambed (Fraley and Shepard 1989; USFWS 1998). Bull trout readily interbreed with non-native brook trout (Salvelinus fontinalis). Brook trout may also exclude bull trout from native habitats (USFWS 1998). Finally, native char are easily caught and are highly susceptible to fishing pressure; therefore, any increase in the accessibility of a population to fishing pressure may negatively impact a population (Fraley and Shepard 1989; USFWS 1998). The USFWS received a petition from an alliance of conservation organizations in Montana to list bull trout throughout its native range under the Endangered Species Act on October 30, 1982. In 1994, the USFWS determined that listing was warranted within the coterminous United States, but was precluded 1145.15.Baker-Bull Trout BA.120502 3-3 Bull Trout and Bald Eagle

due to the need to list higher priority species. Legal debate followed the warranted-but-precluded status from 1995-1997 until populations in the Columbia and Klamath River basin were listed in June 1998. The Coastal-Puget Sound DPS of bull trout was listed as threatened pursuant to the Endangered Species Act on November 1, 1999 (64 Federal Register 58910). Dolly Varden were not listed by the USFWS, but may be listed in the future based on similarity of appearance provisions of the Endangered Species Act (64 Federal Register 58910). The Coastal-Puget Sound bull trout DPS encompasses all Pacific Coast drainages within the coterminous United States north of the Columbia River, and includes 34 subpopulations of native char, 15 of which occur in the Puget Sound analysis area, and four that occur in the Skagit River basin. The Skagit River Basin supports the largest population of native char in Puget Sound. Anadromous, adfluvial, and riverine life history strategies all exist in the watershed, and there is considerable geographical overlap between fish exhibiting different life history patterns. The lower Skagit River bull trout subpopulation is the only one considered strong by the USFWS in the Puget Sound analysis area based on the large number of spawning adults and high overall abundance (64 Federal Register 58910). The status of the other three subpopulations in the Skagit River is unknown because insufficient abundance, trend, and life history information is available. WDFW originally classified bull trout within the Baker Basin reservoirs and tributaries as a distinct stock based on its geographic distribution (WDFW 1998) and classified their status as unknown. However, the Bull Trout Recovery Team reviewed the distribution of Skagit Basin subpopulations, and bull trout within the Baker Basin are now considered to be part of the lower Skagit River subpopulation (C. Kraemer, WDFW, pers. comm. 2002). Both bull trout and Dolly Varden are suspected to occur in Baker Lake and the population may contain adfluvial, resident and riverine life history forms (WDFW 1998). Additional information on native char in the Baker Basin will be developed in the next few years as part of relicensing studies, and as part of ongoing state and federal efforts to meet long-term recovery goals for the Coastal-Puget Sound DPS. There is little information on Baker River bull trout abundance; however, since 1994 PSE has recorded observations of native char collected at the Baker Project fish passage facilities. Information specific to Baker River are scarce. WDFW considered the status of Baker Lake bull trout to be unknown due to the lack of escapement estimates or relative abundance data (WDFW 1998). However, since 1994 PSE has recorded observations of native char collected at the Baker Project fish passage facilities. PSE's upstream and downstream fish passage facilities at the Baker Project (FERC No. 2150) provide the opportunity for movement of bull trout between the Baker River system, the Skagit River, and Puget Sound. PSE has operated an upstream trap and haul fish passage facility at the Baker Project since 1926. The number of native char trapped and hauled above the Baker Project was not recorded prior to 1994. Since 1994, an average of 18 native char per year have been hauled above the Baker Project and released (Table 3-1). Few juvenile bull trout are counted at the Baker Project downstream passage facility, but it is unclear whether this represents undersampling or is indicative of a low rate of downstream movement. Large native char are frequently observed holding at the entrance to the downstream fish passage facilities in both reservoirs during the spring where they prey on outmigrating salmonid juveniles. Large native char are also reported to congregate immediately below Upper Baker Dam (i.e., upper reaches of Lake 1145.15.Baker-Bull Trout BA.120502 3-4 Bull Trout and Bald Eagle

Shannon) during the spring. Three native char were captured during hook-and-line sampling conducted in October 2002 in the canyon at the base of Upper Baker Dam, and it is assumed that some native char utilize this reach on a year-round basis. Snorkel surveys, hook-and-line sampling and the use of baited minnow traps failed to confirm the presence of native char in the 0.6 mile reach between the barrier dam and Lower Baker Dam. Table 3-1 Number of Dolly Varden/bull trout (native char) trapped and hauled above the Baker Project since 1994. Annual counts of native char transported above the Baker Project were not recorded prior to June 1994 (A. Aspelund, PSE, pers. comm. 2002) PERIOD Number of native char hauled and released above Upper Baker Dam June 1994 through May 1995 11 June 1995 through May 1996 27 June 1996 through May 1997 40 June 1997 through May 1998 9 June 1998 through May 1999 12 June 1999 through May 2000 18 June 2000 through May 2001 18 June 2001 through May 2002 7 June 2002 through Nov 8 2002 18 Many tributaries to Lake Shannon are relatively warm, but juvenile char have been observed in Bear Creek and Sulphur Creek that feed into the lower reservoir. In comparison to Lake Shannon tributaries, several Baker Lake tributaries have cold, glacial origins and support apparently robust native char populations. Researchers conducting electrofishing and snorkel surveys in Park Creek found coho, chinook, rainbow and native char in the lower reaches, but on occasion, native char were the predominant species observed in the mile of stream channel immediately below a waterfall that represents a barrier to upstream migration. The Upper Baker River is the largest sub basin draining to Baker Lake, and although accurate numbers are not available, the sub basin appears to support a robust native char population. Large native char, up to 75-cm in length were observed in the Upper Baker River during habitat surveys conducted in the fall of 2001 and 2002. These large fish were presumed to be adfluvial adults migrating into the Baker River from Baker Lake. As part of ongoing relicensing studies, fall snorkeling and angling surveys were 1145.15.Baker-Bull Trout BA.120502 3-5 Bull Trout and Bald Eagle

conducted in the Upper Baker River watershed and numerous native char were observed in pools upstream to a cascade at approximately RM 28. Electrofishing surveys in 1992 had also indicated numerous juvenile native char in side channels near Pass Creek, immediately below RM 28 (Walsh 1992). 3.2.2 Dolly Varden (Salvelinus malma) Bull trout and Dolly Varden are very difficult to distinguish based on physical features and share similar life history traits and habitat requirements (WDFW 1998; 64 FR 58909). Both species have been found to co-exist in streams in this region. These two native char species occur sympatrically in a number of drainages in western Washington, including the Snohomish and Skagit rivers (WDFW 1998). The species composition of native char in most Puget Sound Rivers, including the Baker River, will remain uncertain until a comprehensive genetic analysis of native char populations in this region is completed (WDFW 1998). Much remains to be understood about bull trout and Dolly Varden life histories and the potential interactions between the two species. Some researchers have observed that in some systems where both adfluvial and riverine populations of native char co-exist, Dolly Varden exhibit a riverine life history and are found in the smaller stream systems while bull trout exhibit an adfluvial life history and are found in the reservoirs and larger tributaries (McPhail and Taylor 1995, Taylor et al. 2001). Little information is available on the genetic differences between adfluvial and riverine life history forms of native char in the Baker basin, but until more information is available, no distinction between the species will be made when describing the effects of interim conservation measures. Dolly Varden, were not listed as a threatened species in the DPS when the USFWS listed bull trout in November 1999 (64 FR 58909). However, the USFWS indicated on January 9, 2001 that Dolly Varden are being considered for listing as threatened due to their similarity of appearance to bull trout (66 FR 1628). Because these two species are closely related and have similar biological characteristics, the WDFW manages bull trout and Dolly Varden together as native char (WDFW 2000). Because of similar life history traits and habitat requirements, we have assumed that Dolly Varden are present in the Action Area. 3.2.3 Bald Eagle (Haliaeetus leucocephalus) Bald eagles (Haliaeetus leucocephalus) are large raptors that are found throughout the United States and Canada. While some eagles nest in Washington State, high concentrations of eagles nest along the coastlines of Alaska and Canada migrating south to overwinter along major rivers. Migrant eagles from other states and provinces may arrive in Washington State in late October and stay until early March (Watson and Rodrick 2001). Favored overwintering areas typically support abundant waterfowl and large, late-run salmon populations or other abundant prey items. Bald eagles may roost communally 1145.15.Baker-Bull Trout BA.120502 3-6 Bull Trout and Bald Eagle