J_5_d_NMFS_FWS_BiOPs_Spotted_Owl_LOC.pdf

INTERIOR REGION 9

COLUMBIA–PACIFIC NORTHWEST

Idaho, Montana*, Oregon*, Washington

*PARTIAL

United States Department of the Interior

FISH AND WILDLIFE SERVICE

Central Washington Field Office 215 Melody Lane, Suite 103

Wenatchee, Washington 98801 In Reply Refer To:

01EWFW00-2020-F-0261

Memorandum

To: Environmental Program Manager, Bureau of Reclamation Yakima, Washington

From: State Supervisor, Washington Fish and Wildlife Office Lacey, Washington

Subject: Biological Opinion on the Cle Elum Dam Fish Passage Construction Activities in the Upper Yakima River, Washington

This memorandum transmits the U. S. Fish and Wildlife Service's (Service) Biological Opinion on the proposed Cle Elum Dam Fish Passage Construction Activities in the Upper Yakima River, Washington (Project) located in Kittitas County, Washington, and its effects on bull trout (Salvelinus confluentus), and its designated critical habitat. Formal consultation was conducted in accordance with section 7 of the Endangered Species Act of 1973, as amended (16 U.S.C.

1531 et seq.) (ESA). Your November 07, 2019, request for formal consultation was received on November 12, 2019.

The attached Biological Opinion is based on information provided in the November 7, 2019, Biological Assessment (BA), the May 20, 2020, BA Supplement, telephone conversations, field investigations, and other sources of information as described in the Biological Opinion. A complete record of this consultation is on file at the Service's Central Washington Field Office in Wenatchee, Washington. An electronic copy of this Biological Opinion will be available to the public approximately 14 days after it is finalized and signed. A list of Biological Opinions completed by the Service since October 1, 2017, can be found on the Service’s Environmental Conservation Online System (ECOS) website at https://ecos.fws.gov/ecp/report/biological-opinion.html.

for JEFFREY

KRUPKA

Digitally signed by

JEFFREY KRUPKA

Date: 2021.02.05 17:03:00 -08'00'

If you have any questions regarding the attached Biological Opinion or our shared responsibilities under the Endangered Species Act, please contact my staff Stephen Lewis at 509- 665-3508 ext. 2002 or Jeff Krupka at 509-665-3508 ext. 2008.

Attachment cc:

BOR, Yakima, WA (S. Willey) BOR, Yakima, WA (R. Visser) FWS, Yakima, WA (J. Romine) NOAA, Ellensburg, WA (S. Gross)

Endangered Species Act - Section 7 Consultation

BIOLOGICAL OPINION

U.S. Fish and Wildlife Service Reference:

01EWFW00-2020-F-0261

Cle Elum Dam Fish Passage Construction Activities in the Upper Yakima River, Washington

Kittitas County, Washington

Federal Action Agency:

Bureau of Reclamation

Consultation Conducted By:

U.S. Fish and Wildlife Service Washington Fish and Wildlife Office

Wenatchee, Washington

Brad Thompson, State Supervisor Date Washington Fish and Wildlife Office for

JEFFREY KRUPKA

Digitally signed by JEFFREY

KRUPKA

Date: 2021.02.05 17:03:55 -08'00' ii

TABLE OF CONTENTS

1 INTRODUCTION

2 CONSULTATION HISTORY

3 BIOLOGICAL OPINION

4 DESCRIPTION OF THE PROPOSED ACTION

4.1 Conservation Measures

4.2 Action Area

5 ANALYTICAL FRAMEWORK FOR THE JEOPARDY AND ADVERSE

MODIFICATION DETERMINATIONS

5.1 Jeopardy Determination

5.2 Adverse Modification Determination

6 STATUS OF THE SPECIES: Bull Trout 7 STATUS OF CRITICAL HABITAT: Bull Trout 8 ENVIRONMENTAL BASELINE: Bull Trout and Designated Bull Trout Critical

Habitat

8.1 Current Condition of the Species and Critical Habitat in the Action Area

8.1.1 Current Condition of Bull Trout in the Yakima Core Area and Action Area

8.1.2 Current Condition of Critical Habitat in the Action Area

8.1.3 Factors Responsible for the Condition of Bull Trout

8.1.4 Factors Responsible for the Condition of Bull Trout Critical Habitat

8.2 Conservation Role of the Action Area

8.3 Climate Change

9 EFFECTS OF THE ACTION: Bull Trout and Designated Bull Trout Critical Habitat

9.1 Effects to Adult and Sub-Adult Bull Trout from Stilling Basin Dewatering and Fish Salvage for Splitter Wall Construction

9.2 Effects to Fry and Juvenile Bull Trout from Stilling Basin Dewatering and Fish Salvage

9.3 Effects to Bull Trout from the Construction and Long-Term Operation of the Cle Elum Fish Passage Facilities

9.3.1 Construction and Long-Term Operation of Adult Collection Facility

9.3.2 Long-Term Operation of Downstream Passage Facilities

9.4 Effects to Bull Trout Designated Critical Habitat in the Yakima River Core Area from the Proposed Action

9.4.1 Description of Effects to Designated Bull Trout PCEs from the Proposed Action

9.5 Summary of Effects

10 CUMULATIVE EFFECTS: Bull Trout and Designated Bull Trout Critical Habitat 11 INTEGRATION AND SYNTHESIS OF EFFECTS: Bull Trout and Designated Bull

Trout Critical Habitat

11.1 No Jeopardy Determination

11.2 No Adverse Modification Determination

iii

12 CONCLUSION: Bull Trout and Designated Bull Trout Critical Habitat

13 INCIDENTAL TAKE STATEMENT

14 AMOUNT OR EXTENT OF TAKE

15 EFFECT OF THE TAKE

16 REASONABLE AND PRUDENT MEASURES

17 TERMS AND CONDITIONS

18 CONSERVATION RECOMMENDATIONS

19 REINITIATION NOTICE

20 LITERATURE CITED

Appendices

Appendix A Status of the Species: Bull Trout Appendix B Status of Designated Critical Habitat : Bull Trout

FIGURES

Figure 1. Illustration of the Cle Elum Fish Passage Project, highlighting the juvenile fish passage facility components Figure 2. Map of the federal action area for the consultation. The action area encompasses the entire Cle Elum watershed because Reclamation is covering the long-term operation and maintenance of the adult and juvenile fish passage facilities in this consultation

Figure 3. Upper Yakima drainage showing known bull trout distribution and spawning areas

TABLES

Table 1. Summary of Bull Trout redd counts in the Yakima basin, 1984-2017 Table 2. Habitat delineations for PCE analysis for those bull trout local populations affected by the proposed action Table 3. Bull trout critical habitat PCEs – baseline conditions in the Cle Elum Watershed Table 4. The anticipated lethal and non-lethal incidental take of bull trout by Project

Element iv

ACRONYMS AND ABBREVIATIONS

BA Biological Assessment BMP Best Management Practices CFR Code of Federal Regulations cfs cubic feet per second ESA Endangered Species Act of 1973, as amended (16 U.S.C. l531 et seq.)

Service U.S. Fish and Wildlife Service USFS U.S. Forest Service WDOE Washington State Department of Ecology CH Critical Habitat CHU Critical Habitat Unit CM Conservation Measure CNF Colville National Forest COC contaminants of concern Corps U.S. Army Corps of Engineers County Kittitas County DAM Destruction or Adverse Modification DPS Distinct Population Segment EA Environmental Assessment EIS Environmental Impact Statement FEIS Final Environmental Impact Statement FMO Foraging, Migration and Overwintering FR Federal Register ft2 square feet IGDO inter-gravel dissolved oxygen IPCC Intergovernmental Panel on Climate Change IRU Interim Recovery Unit km2 square kilometers LWD Large Woody Debris MCFWRO Mid-Columbia Fish and Wildlife Resources Office MHHW mean higher high-water NMFS National Marine Fisheries Service NTU Nephelometric turbidity units Opinion Biological Opinion PBF Physical or Biological Features PCE Primary Constituent Element Project Cle Elum Fish Passage Project RPM Reasonable and Prudent Measures Reclamation Bureau of Reclamation Service U.S. Fish and Wildlife Service TDG Total Dissolved Gas WDFW Washington Department of Fish and Wildlife WFWO Washington Fish and Wildlife Office WQS Water Quality Standards

1 INTRODUCTION

This document represents the U. S. Fish and Wildlife Service's (Service) Biological Opinion (Opinion) based on our review of the proposed Cle Elum Dam Fish Passage Construction Activities (Project) located in Kittitas County, Washington. The Opinion addresses effects to bull trout (Salvelinus confluentus) and its designated critical habitat in accordance with section 7 of the Endangered Species Act of 1973, as amended (16 U.S.C. 1531 et seq.) (ESA). Your November 7, 2019, request for formal consultation was received on November 12, 2019.

This Opinion is based on information provided in the November 4, 2019, BA, (Bureau of Reclamation (Reclamation) 2019), the May 20, 2020, Supplemental BA (Reclamation 2020), telephone conversations, field investigations, and other sources of information as detailed below.

A complete record of this consultation is on file at the Service's Central Washington Field Office in Wenatchee, Washington.

2 CONSULTATION HISTORY

The following is a summary of important events associated with this consultation:

• The BA was received on November 12, 2019.

• Formal consultation was initiated on December 03, 2019.

• An extension of consultation request was submitted to Reclamation on March 3, 2020.

• The BA Supplement was received by the Service electronically on May 20, 2020.

3 BIOLOGICAL OPINION

4 DESCRIPTION OF THE PROPOSED ACTION

A Federal action means all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies in the United States or upon the high seas (50 CFR 402.02).

The purpose of the Cle Elum Dam Fish Passage Project (Project) is to construct a concrete splitter wall within the stilling basin of Cle Elum Dam and to complete the excavation of the right bank adult collection facility foundation including all appurtenant adult and juvenile fish passage structure water connections with the Cle Elum Dam stilling basin (e.g. juvenile fish bypass pipe outfall and the adult fish ladder entrance). In order to complete these construction activities, the Project will require short term flow alterations to the Cle Elum River, cofferdam construction, site dewatering, fish salvage and recovery, water management (continuous dewatering) and in-channel and stream bank construction actions (Figure 1). Consultation is also requested for the long term operation and maintenance activities of the proposed fish passage facilities once they become fully operational.

The proposed construction actions and sequencing for the Project are as follows:

• Install dewatering wells in upland areas on the south (right) bank of the stilling basin.

• Begin process of reducing Cle Elum Dam water releases to 500 cfs by September 1-10.

• Install a temporary Helix bypass pipe on the right (south) bank of the stilling basin that is attached to the existing Cle Elum juvenile fish passage tunnel outlet and construct an ecology block lined plunge pool at the outlet location of the Helix bypass.

• Install a temporary crane pad on the left (north) bank of the stilling basin downstream of the dam outlet works.

• Place the Cle Elum Dam outlet works diversion conduit in stilling basin near dam outlet works.

• Construct a channel spanning cofferdam approximately 500 feet downstream of stilling basin concrete apron and install cofferdam deep groundwater pumping wells. The cofferdam will be constructed using multiple spawning-sized gravel filled Super Sacks or a series of water-filled bladders with packed spawning-sized gravels on the upstream side.

• Connect the outlet works diversion conduit to dam outlet works after cofferdam is completed.

• Begin dewatering stilling basin by bypassing water through Cle Elum Dam outlet works diversion conduit and operating dewatering wells and pumps.

• Conduct fish salvage operations prior to complete dewatering of stilling basin work area

• Construct vehicle access road into stilling basin work area from left bank.

• Construct concrete splitter wall structure and repair stilling basin concrete.

• Excavate foundation for adult fish collection facility on left bank.

• Demolish portions of right (south) bank abutment wall and construct adult and juvenile fish passage facility connections with stilling basin.

• Relocate rip-rap within stilling basin and construct right (south) bank support wall.

• Remove dewatering system, access road, crane pad, cofferdam, and outlet works diversion conduit.

• More detailed information on the proposed action can be in the following documents:

BA pages 10-36 (Reclamation 2019) and the BA Supplement pages 1-37 (Reclamation 2020).

Figure 1. Illustration of the Cle Elum Fish Passage Project, highlighting the juvenile fish passage facility components Note that the long-term operation of the juvenile and adult facilities and the construction of the Project components downstream of the dam outlet and spillway are the focus of this consultation (Reclamation 2019, p. 3).

4.1 Conservation Measures

The proposed action includes a list of conservation measures (CMs) that Reclamation will employ to avoid or minimize potential environmental impacts and Project effects on ESA listed species and their designated critical habitats during implementation of the Project (Reclamation 2019, Section 2.0 Project Description, pp. 10-36 and Reclamation 2020, Section 2.0 Proposed Action Description, pp. 1-37). We refer to specific CMs in our effects analysis.

4.2 Action Area

The action area is defined as all areas to be affected directly or indirectly by the federal action and not merely the immediate area involved in the action (50 CFR 402.02). In delineating the action area, we evaluated the farthest reaching physical, chemical, and biotic effects of the action on the environment. The action area for this proposed federal action is based on the geographic extent of upstream passage and the farthest reaching stressor, which is sediment, downstream.

The action area for this proposed action therefore includes the immediate construction area for the proposed Project which will extend downstream of the dam for a distance of approximately 1,000 linear feet, the Cle Elum River downstream to its confluence with the Yakima River, and the area within and upstream of Cle Elum Reservoir and the 26 miles of stream habitat that would be made accessible to migratory or adfluvial fish upstream of the dam. Figure 2 shows the approximate federal action area within the Cle Elum River watershed for this proposed action.

Figure 2. Map of the federal action area for the consultation. The action area encompasses the entire Cle Elum watershed because Reclamation is covering the long-term operation and maintenance of the adult and juvenile fish passage facilities in this consultation

5 ANALYTICAL FRAMEWORK FOR THE JEOPARDY AND ADVERSE

MODIFICATION DETERMINATIONS

5.1 Jeopardy Determination

In accordance with policy and regulation, the jeopardy determination in this Biological Opinion relies on the following components:

The Status of the Species, which evaluates the species’ range-wide condition relative to its reproduction, numbers, and distribution, the factors responsible for that condition, and its survival and recovery needs.

The Environmental Baseline, which evaluates the condition of the species in the action area relative to its reproduction, numbers, and distribution without the consequences caused by the proposed action, the factors responsible for that condition, and the relationship of the action area to the survival and recovery of the species.

The Effects of the Action, which evaluates all future consequences to the species that are reasonably certain to be caused by the proposed action, including the consequences of other activities that are caused by the proposed action, and how those impacts are likely to influence the conservation role of the action area for the species; and

Cumulative Effects, which evaluates the consequences of future, non-Federal activities reasonably certain to occur in the action area on the species, and how those impacts are likely to influence the conservation role of the action area for the species.

In accordance with policy and regulation, the jeopardy determination is made by evaluating the consequences of the proposed Federal action in the context of the species’ current range-wide status, taking into account any cumulative effects, to determine if implementation of the proposed action is likely to cause an appreciable reduction in the likelihood of both the survival and recovery of the species in the wild. The key to making this finding is clearly establishing the role of the action area in the conservation of the species as a whole, and how the effects of the proposed action, taken together with cumulative effects, are likely to alter that role.

5.2 Adverse Modification Determination

A final rule revising the regulatory definition of “destruction or adverse modification” (DAM) of critical habitat (CH) was published on August 27, 2019 (84 FR 44976). The final rule became effective on October 28, 2019. The revised definition states:

“Destruction or adverse modification means a direct or indirect alteration that appreciably diminishes the value of critical habitat as a whole for the conservation of a listed species.”

In accordance with policy and regulation, the destruction or adverse modification determination in this Biological Opinion relies on the following components:

The Status of Critical Habitat, which describes the range-wide condition of the CH in terms of essential habitat features, primary constituent elements, or physical and biological features that provide for the conservation of the listed species, the factors responsible for that condition, and the intended value of the CH as a whole for the conservation/recovery of the listed species;

The Environmental Baseline, which refers to the condition of CH in the action area (without the consequences to CH caused by the proposed action), the factors responsible for that condition, and the conservation value of CH in the action area for the conservation/recovery of the listed species;

The Effects of the Action, which represents all consequences to CH that are reasonably certain to be caused by the proposed action, including the consequences of other activities that are caused by the proposed action, and how those impacts are likely to influence the conservation value of the affected CH; and

Cumulative Effects, which represent the consequences of future non-Federal activities that are reasonably certain to occur in the action area and how those impacts are likely to influence the conservation value of the affected CH.

For purposes of making the DAM determination, the Service evaluates if the effects of the proposed Federal action, taken together with cumulative effects, are likely to impair or preclude the capacity of CH as a whole to serve its intended conservation function for the conservation of the listed species. The key to making this finding is clearly establishing the role of CH in the action area relative to the value of CH as a whole, and how the effects of the proposed action, taken together with cumulative effects, are likely to alter that role.

6 STATUS OF THE SPECIES: Bull Trout

The bull trout was listed as a threatened species in the coterminous United States in 1999.

Throughout its range, the bull trout is threatened by the combined effects of habitat degradation, fragmentation, and alteration (associated with dewatering, road construction and maintenance, mining, grazing, the blockage of migratory corridors by dams or other diversion structures, and poor water quality), incidental angler harvest, entrainment, and introduced non-native species (64 FR 58910 [Nov. 1, 1999]). Since the listing of bull trout, there has been very little change in the general distribution of bull trout in the coterminous United States, and we are not aware that any known, occupied bull trout core areas have been extirpated (USFWS 2015b, p. iii).

The 2015 recovery plan for bull trout identifies six recovery units of bull trout within the listed range of the species (USFWS 2015b, p. 34). Each of the six recovery units are further organized into multiple bull trout core areas, which are mapped as non-overlapping watershed-based polygons, and each core area includes one or more local populations. Within the coterminous United States we currently recognize 109 currently occupied bull trout core areas, which comprise 600 or more local populations (USFWS 2015b, p. 34). Core areas are functionally similar to bull trout meta-populations, in that bull trout within a core area are much more likely to interact, both spatially and temporally, than are bull trout from separate core areas.

The Service has also identified a number of marine or main-stem riverine habitat areas outside of bull trout core areas that provide foraging, migration, and overwintering (FMO) habitat that may be shared by bull trout originating from multiple core areas. These shared FMO areas support the viability of bull trout populations by contributing to successful overwintering survival and dispersal among core areas (USFWS 2015b, p. 35).

For a detailed account of bull trout biology, life history, threats, demography, and conservation needs, refer to Appendix A: Status of the Species: bull trout.

7 STATUS OF CRITICAL HABITAT: Bull Trout

Bull trout critical habitat was designated in the coterminous United States in 2010. The condition of bull trout critical habitat varies across its range from poor to good. Although still relatively widely distributed across its historic range, the bull trout occurs in low numbers in many areas. Overall bull trout abundance is "stable" range-wide (USFWS 2015b, p. iii).

However, 81 core areas have 1,000 or fewer adults, with 24 core areas not having surveys conducted to determine adult abundance (USFWS 2008a, p. 22; USFWS 2015a, p. 2). In addition, 23 core areas have declining populations, with 66 core areas having insufficient information (USFWS 2008a, p. 22; USFWS 2015a, p. 2). These values reflect the condition of bull trout habitat. The decline of bull trout is primarily due to habitat degradation and fragmentation, blockage of migratory corridors, poor water quality, past fisheries management practices, impoundments, dams, water diversions, and the introduction of nonnative species (63 FR 31647, June 10 1998; 64 FR 17112, April 8, 1999).

There is widespread agreement in the scientific literature that many factors related to human activities have impacted bull trout and their habitat, and continue to do so. Among the many factors that contribute to degraded the PCEs, those that appear to be particularly significant and have resulted in a legacy of degraded habitat conditions are as follows:

1. fragmentation and isolation of local populations due to the proliferation of dams and water diversions that have eliminated habitat, altered water flow and temperature regimes, and impeded migratory movements (Dunham and Rieman 1999, p. 652; Rieman and McIntyre 1993, p.7);

2. degradation of spawning and rearing habitat and upper watershed areas, particularly alterations in sedimentation rates and water temperature, resulting from forest and rangeland practices and intensive development of roads (Fraley and Shepard 1989, p.

141; The Montana Bull Trout Scientific Group (MBTSG) 1998, pp. ii-v, 20-45);

3. the introduction and spread of nonnative fish species, particularly brook trout (S.

fontinalis) and lake trout (S. namaycush), as a result of fish stocking and degraded habitat conditions, which compete with bull trout for limited resources and, in the case of brook trout, hybridize with bull trout (Leary et al. 1993; Rieman et al. 2006);

4. in the Puget Sound and Olympic Peninsula geographic regions where anadromous bull trout occur, degradation of main-stem river FMO habitat, and the degradation and loss of marine nearshore foraging and migration habitat due to urban and residential development; and

5. degradation of FMO habitat resulting from reduced prey base, roads, agriculture, development, and dams.

For a detailed account of the status of the designated bull trout critical habitat, refer to Appendix B: Status of Designated Critical Habitat: bull trout

8 ENVIRONMENTAL BASELINE: BULL TROUT AND DESIGNATED BULL

TROUT CRITICAL HABITAT

Regulations implementing the ESA (50 CFR 402.02) define the environmental baseline as the condition of the listed species or its designated critical habitat in the action area, without the consequences to the listed species or designated critical habitat caused by the proposed action.

The environmental baseline includes the past and present impacts of all Federal, State, or private actions and other human activities in the action area, the anticipated impacts of all proposed Federal projects in the action area that have already undergone formal or early section 7 consultation, and the impact of State or private actions which are contemporaneous with the consultation in process. The consequences to listed species or designated critical habitat from ongoing agency activities or existing agency facilities that are not within the agency’s discretion to modify are part of the environmental baseline.

8.1 Current Condition of the Species and Critical Habitat in the Action Area

8.1.1 Current Condition of Bull Trout in the Yakima Core Area and Action Area

Bull trout are distributed throughout the Yakima River Basin. The number of recognized local populations in the Yakima Basin has shifted over time (Reiss et al. 2012). At the time of listing, the Service identified eight small subpopulations in the Yakima River Basin. The 2002 draft recovery plan for the Yakima Core Area (USFWS 2002) recognized 13 local bull trout populations. The Bull Trout Action Plan (Reiss et al. 2012) described 16 local populations, and based on further genetics work, the Final Bull Trout Recovery Plan (USFWS 2015) describes 15 local populations. These include four fluvial populations (mainstem Yakima River, American River, Crow Creek, and Rattlesnake Creek), two resident populations (North Fork Teanaway River and Ahtanum Creek), and nine adfluvial populations (Gold Creek, Box Canyon Creek, Kachess River, Cle Elum River, Indian Creek, South Fork Tieton River, North Fork Tieton River, Bumping River (includes Deep Creek), and Waptus Lake). More recently, bull trout have been captured at various locations in the mainstem Yakima River and redds have been observed in the upper Yakima River between Keechelus Dam and Lake Easton. Bull trout abundance in the Yakima Core Area has been tracked primarily through redd surveys conducted on index reaches in spawning areas. There is comparable data from redd surveys in the Yakima Core Area from 1984 through 2017 (Table 1).

Table 1. Summary of Bull Trout redd counts in the Yakima basin, 1984-2017 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99

09 10 11 12 13

Yakima River (F) Keechelus to Easton Reach * 2

3 1

Ahtanum Creek (R) N.F. Ahtanum Cr. 9 14 6 5 7 5 7 11 20 17 12 8 6 7 8 1

3 0 1

0 2 2 (Shellneck Cr.)

M.F. Ahtanum Cr. * 1

6 8 11 5 6 5 3

9 15 11 8

7 6 4 6 9 S.F. Ahtanum Cr. * 5

14 13 7 5 3 4 5

6 2 4 2 1 2 0 0 0 Naches River (F) Rattlesnake Cr. * 2

26 38 46 53 44 45 57 69 54 32 15 40 13 37 36 64 42 42 32 23 28 15 18 (L.Wildcat Cr., Shell Cr.)

American R. 25 24 31 30 44 36 27 30 40 35 55 31 22

29 47 40 54 54 37

31 30 9 (Union Cr., Kettle Cr.)

Crow Cr. 19 26 6 9 9 6 4 8 8

5 9

2 5 7

Rimrock Lake (AD) S.F. Tieton R. * 32

167 95

142 161 144 158 141 178

178 205 189 152 266 259 194 234 226 151 192 160 162 191 (Bear Cr.)

Indian Cr. *

35 25 39 69 123 142 140 179 201 193 193 212 205 226 117 100 101 50 91 106 58

130 200 144 147 174 10

28 49 38 37 (+spring tribs)

N.F. Tieton (upper)* 1

37 28 15 18 11 17 10 19 27 21 39 (Hellbender Cr.)

Bumping Lake (AD)

Deep Cr. * 17

84 78 45 12 101 46 126 98 107 147 51 120 57 97 73 95 130 145 178 199 192 169 108 78 22 46 59 Bumping River (upper) 1

2 0 0

N.F. Teanaway River (F/R)

NF Teanaway/DeRoux Cr. * 2

1 0 0 1 0 0 0 1 0

Kachess Lake (AD)

Box Canyon Cr. 5 4 3 0 0 0 5 9 5 4 11 4 8 10 16 17 10 14 15 8 19 8 8 2

21 30 31 9 6 10 8 7 3 Kachess R (upper) * 0

15 14 0 16 8 3

22 2 2 15 33 8 13 9 5 9 19 Keechelus Lake (AD)

Gold Cr. 2 2 21 15 12 3 11 16 14 11 16 13 51 31 36 40 19 15 31 9 20 7 8 6

29 23 7 7 12 19 3 5 2 Cle Elum & Waptus Lks (AD)

Cle Elum R.(up) & Waptus R* 0

0 0 0 0 0 0 0 0

Summary 36 75 40 50 37 59 134 232 239 247 404 446 595 615 593 630 704 504 548 490 475 457 531 478 687 795 760 760 727 412 426 342 350 388

* Incomplete survey; index area not fully defined or adequately monitored: Yakima R. spot checks, all years. M.F. Ahtanum 1996-2001, 2008, 2012. S.F. Ahtanum 2000.

Rattlesnake 1990-1995, 2007, 2008, 2011, 2012, 2016, 2017. S.F. Tieton 1990-1993,1995, 2010, 2013, Indian 1984-1987, 2013, Deep 1989-1990, N.F. Teanaway 1996, 2005, 2006, 2008.

Kachess 1998, 2005, 2006, 2012, 2015. Cle Elum 1996, 2000-2002, 2006, 2007, Waptus 1997,1998, N.F. Tieton 2004, 2006, 2010, 2013, 2014. Bumping 1994, 2000, 2004, 2008.

Box 2007, 2012, 2014, 2016. Gold 2007, 2012, 2014, 2016. Crow 2017. (Redds in small tribs (parenthesis) included in total stream count.)

S.F. Tieton redd counts outside of the standard index not included in above totals: 1995=0, 1996=7, 1997=1, 1998-2002 not checked, 2003=14, 2004=2, 2005=6, 2006=22 2007 & 2008 not checked, 2009=30, 2010=6, 2011=19, 2012=33, 2013=11, 2014=4, 2015=10, 2016=7, 2017=17. Exploratory redd survey lower Bumping in 2014 - 0, Lower Crow 2015 - 0.

Exploratory redd count surveys conducted in 2009: N.F. Little Naches - 0, Quartz & N.F. Quartz - 0, Nile - 0, upper Crow (above barrier falls) - 0. 2015 - Lower SF Tieton - 0 redds.

(Data from WDFW, Eric Anderson, Personal Communication, 2017)

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Based on information from the Service’s 2015 Final Bull Trout Recovery Plan (USFWS 2015) and the WDFW’s 1992 Salmon and Steelhead Stock Inventory information (WDFW 1992), the upper Yakima River Basin consists of several local populations including the Yakima River, Kachess Reservoir, Keechelus Reservoir, Teanaway River, and Cle Elum/Waptus River local populations. Figure 3 shows the current bull trout distribution and confirmed spawning areas in the Upper Yakima River basin. This map provides the most up to date information on bull trout usage of the upper Yakima River system. The action area occurs in the Yakima Core Area and includes the Cle Elum Reservoir and Waptus Lake populations.

Figure 3. Upper Yakima drainage showing known bull trout distribution and spawning areas (Reclamation 2019, p. 53)

Cle Elum Reservoir Population

Cle Elum Lake has a large and diverse watershed consisting of the main Cle Elum River and five major tributary streams (Flagg et al. 2000). The largest of these tributaries are the Cooper and Waptus rivers. There is a substantial amount of potential habitat in the drainage, but some of it may be inaccessible to migratory salmonids including bull trout due to barrier falls which exist on these rivers. While these falls may impede further upstream migration of the adfluvial population which resides in Cle Elum Lake, they would not preclude the possibility that other local populations exist in the watershed which display the fluvial/resident life history form.

Lake Cle Elum bull trout became isolated from other Yakima River local populations after the construction of the current dam on Lake Cle Elum in 1933. The dam currently restricts migration between the Cle Elum River stock and other Yakima basin stocks of bull trout. The fluvial form may have been present historically, although currently very few are encountered in the mainstem Yakima River below the Cle Elum drainage (USFWS 2001).

The Cle Elum River population is defined as bull trout that may be present in the mainstem upper Cle Elum River and its tributaries. Both adult and juvenile bull trout have been found in the upper Cle Elum River, but no redds have been documented in the river or any of its tributaries. Redd surveys have been sporadic and incomplete. It is probable that adfluvial bull trout were present in Cle Elum Reservoir following the construction of the dam, but little data exist regarding bull trout population status after dam construction. No bull trout redds have been confirmed in surveys that have been conducted in the Cle Elum River or Waptus/Waptus Lake areas since 2000 (Table 5).

In 1996, biologists from Central Washington University observed several adult bull trout during a snorkel survey below Salmon La Sac Bridge (Craig 1996, as cited in Reiss et al. 2012). This bridge is located between the Cle Elum and Cooper Rivers. Because of their size (reported as “large”), the observers speculated that they might be migrating adfluvial fish. In 2002, two adult bull trout were observed by Service snorkelers just below a potential barrier; however, these fish were not of the size characteristic of adfluvial adults. No bull trout were sighted in the Cle Elum River or French Cabin Creek during snorkel surveys conducted in September 1998 (USFWS 1998). The Service conducted a study in the summer of 2002 to confirm presence/absence of bull trout and identify spawning areas in the upper Cle Elum drainage and Fortune Creek.

Twenty-four juvenile bull Trout (<150mm) and 2 adult Bull Trout (>220mm) were observed through underwater observations during this sampling effort (USFWS 2003). Adfluvial bull trout in Lake Cle Elum were last observed during netting associated with the Sockeye Salmon Reintroduction Feasibility Study conducted by the National Marine Fisheries Service (NMFS) between 1989 and 1993 (Flagg et al. 2000). During the Flagg et al. 2000 study, a total of 17 bull trout ranging in size from 6 to 16 inches, were captured in traps set in the lake (USFWS 2001).

A night snorkel survey covering several reaches of the upper Cle Elum River watershed was conducted by the Service, U.S. Forest Service, WDFW, Yakama Nation, and Reclamation personnel in 2008. This survey failed to locate bull trout in the upper Cle Elum watershed.

Finally, no bull trout were caught during Yakama Nation efforts to remove lake trout (Salvelinus namaycush) in the fall and winter of 2013/2014. In summary, it is uncertain if a viable adfluvial bull trout population still inhabits Cle Elum Reservoir; it is also unknown if a resident component exists in the upper Cle Elum River.

The status of the Cle Elum and Waptus bull trout populations are currently classified as “unknown” by the WDFW (WDFW 1998 and WDFW 2004) and as “depressed and declining” by the Service (USFWS 1998, USFWS 2008; USFWS 2002, USFWS 2015) due to insufficient data on adult abundance, spawning success or juvenile production. This stock is considered to be adfluvial with adults inhabiting the reservoir for most of the year and presumably using the upper Cle Elum River and the Waptus River for spawning and juvenile rearing. The Cle Elum and Waptus Rivers are separated spatially and the Waptus population has access to its own Waptus Lake. It is believed that they are separate populations due to distance, access to a lake, and potential barriers. It is believed that bull trout from these areas enter their spawning streams from August to early October and spawn from mid-September through mid-October in this population segment (WDFW 1998); however, the migration and spawn timing for this stock has not been definitively determined because few redds have ever been found and bull trout spawning activity has not been observed with sufficient frequency to make this determination in the Cle Elum drainage.

It is now believed that the bull trout population in the drainage have been severely reduced (USFWS 2002 and USFWS 2015). Historical catch records indicate that bull trout existed in Waptus Lake in the 1940s and 1950s. More recent work has found that at least some bull trout still inhabit Waptus Lake, the Cooper River and Cle Elum Lake (USFWS 1998 and USFWS 2008). Photos have been observed in social media that show fishermen catching fish that look like hybrids (Eric Anderson, WDFW, personal communication, 2015). The Cle Elum and Waptus populations may be separate populations, but genetic data required to make this determination are lacking at this time. Historically, there has only been one local population of bull trout officially recognized in this large and diverse watershed. However, the Service has recently indicated that they believe two local populations exist; one in the Cle Elum River and the other consisting of the Waptus River local population.

There has been increased concern about interbreeding and hybridization between bull trout and brook trout (S. fontinalis) that have become prevalent in the Cle Elum watershed and other Yakima River drainages. All snorkel surveys and some redd surveys conducted by the Service have confirmed the presence of brook trout in survey reaches (USFWS 1998 and USFWS 2003).

During the snorkel survey assessment of the upper Cle Elum drainage in 2003, one suspected juvenile bull trout was collected for genetic analysis. The genetic analysis confirmed that this specimen was an F2 hybrid cross between bull and brook trout spawners (Jeff Thomas, USFWS, personal communication, 2004; USFWS 2004). The Service has concluded that many of the bull trout reported during the 1998 and 2002 snorkel surveys may in fact be bull trout/brook trout hybrids (Jeff Thomas, USFWS, personal communication, 2004). The snorkel survey that was conducted in 2008 found that the upper Cle Elum River has a large population of brook trout that could easily hybridize with any bull trout present.

Although there is uncertainty about both historic and current bull trout distribution within the Cle Elum watershed, two potential local bull trout populations, one spawning in the Cle Elum River and the other spawning in Waptus River above Waptus Lake, are currently recognized. It is uncertain if these bull trout populations have persisted. No bull trout have been observed within the Cle Elum Basin since 2003. Recent efforts on behalf of the Mid-Columbia Fisheries Enhancement Group to collect eDNA samples have been completed in the Cle Elum Basin area.

The samples were positive for the presence of fish although very few of these samples were evident for bull trout. Analysis suggests that these positive samples are from the few remaining bull trout that utilize Waptus Lake and the Waptus River rather than the Cle Elum Reservoir (e-mail correspondence, Connor Parrish, Mid-Columbia Fisheries Enhancement Group, 4/29/20).

Recent monitoring efforts demonstrate the potential for bull trout presence below the Cle Elum Dam in the action area. Bull trout that have been observed in the upper Yakima River may be fish that have been entrained over dams and cannot return to upstream spawning areas and now spawn, or attempt to spawn, in the upper Yakima mainstem. For example, these recent monitoring efforts by the Service resulted in the sampling of an adult bull trout below Keechelus Dam which originated from Box Canyon Creek in the Kachess Reservoir outside the action area (e-mail correspondence, Jason Romine, USFWS, 4/29/20). These monitoring efforts also suggest that approximately four adult or sub-adult bull trout may currently reside below Cle Elum Dam based on this evidence of long-range movements (e-mail correspondence, Jason Romine, USFWS, 4/29/20).

Waptus Lake Population

It is believed that Waptus Lake once supported a healthy and likely distinct population of adfluvial bull trout. At this point, the evidence suggests that although some bull trout may persist in Waptus Lake, hybrids seem to be observed by fishermen. It is unknown if a viable population exists due to a lack of surveys and difficult terrain for surveying. It is could be that a local adfluvial and resident component exists in the Waptus subbasin.

The Waptus Lake population includes bull trout present in Waptus Lake, the Waptus River above the lake, and the river below the lake (i.e., above a barrier waterfall occurring at about river mile 2.5). The Waptus River is the larger of the two major tributaries of the upper Cle Elum River, entering the river about 5.5 miles above Cle Elum Lake. The Waptus originates as the outflow from several lakes high in the Alpine Lakes Wilderness about two miles upstream of Waptus Lake. From the outlet of Waptus Lake, the river flows for approximately 8.5 miles to its confluence with the upper Cle Elum River.

This population was last officially rated while combined with Cle Elum Lake. The Service (1998) considered the Cle Elum/Waptus River population to be depressed, decreasing, and at risk of stochastic extirpation. The WDFW rates the status of this stock as unknown (WDFW 2004).

For the purposes of this document the status of the Waptus population should be considered unknown. However, in the Service’s 2015 Final Bull Trout Recovery Plan (USFWS 2015), we concluded that this population was functionally extirpated.

Very few bull trout redd surveys have been conducted in the Waptus River. These include incomplete surveys conducted by WDFW in 1997 to 1998 and a single survey in the reach below the barrier waterfall conducted by the Service in 2003. Also in 2003, the Service conducted a redd survey in a reach extending from Waptus Lake upstream approximately 0.6 miles. No bull trout redds were observed in any of these surveys (USFWS 2004).

8.1.2 Current Condition of Critical Habitat in the Action Area

The Service first issued proposed critical habitat rules for several mainstem and tributary reaches of the Yakima River Basin in November 2002 (FR 67 71235). In October 2004 the Service designated a wide area of bull trout critical habitat: 1,748 miles of stream habitat and 61,235 acres of lakes and marshes within the Klamath and Columbia River basins (69 FR 59995). For the Middle Columbia River Basin (Critical Habitat Unit 20), critical habitat designations were listed for 269 stream miles, all within the Yakima River Basin. In September 2005, the Service issued a revised final designation for bull trout critical habitat and reduced the amount of critical habitat designated in the Middle Columbia River Basin to 188 stream miles (70 FR 56212). In response to a lawsuit, the Service voluntarily remanded the 2005 final rule, and on October 18, 2010, issued the final rule for the revised critical habitat designation for bull trout in the coterminous United States (75 FR 63897).

The final designated critical habitat rule issued in 2010 increased designated stream habitat by three percent relative to that designated in 2004 (75 FR 2270). Under the new final rule, Critical Habitat Units are organized by Recovery Units, with the Mid-Columbia Recovery Unit including the Yakima River (Critical Habitat Unit 11). The 2010 listing identifies the Yakima River as a critical habitat unit, with 557.3 stream miles and 15,530.9 acres of lakes and reservoirs designated as critical habitat. The mainstem Yakima River and the Kachess and Cle Elum rivers below their respective reservoirs are included in the designation. Key reservoirs and reservoir tributaries also designated as critical habitat in the 2010 final designation include Keechelus, Kachess, and Cle Elum Reservoirs, as well as Box Canyon Creek, the Kachess River and Mineral Creek up to natural waterfalls in these systems upstream of Kachess Dam, and Gold Creek up to a natural waterfall fish passage barrier upstream of Keechelus Dam.

The final critical habitat designation in 2010 (75 FR 63897) lists a total of nine primary PCEs that are designed to incorporate what is essential for bull trout conservation in the Klamath River and Columbia River basins. PCEs include, but are not limited to: space for individual and population growth, and for normal behavior; food, water, air, light, minerals, or other nutritional or physiological requirements; cover or shelter; sites for breeding, reproduction, and rearing (or development) of offspring; and habitats that are protected from disturbance (69 FR 59995). The nine PCEs listed in the final rule include water temperature, channel complexity, substrate quality, hydrology, springs/seeps/groundwater, migratory corridors, food base, competition, and permanent water sources.

The action area for this consultation contains FMO areas for the local bull trout populations located both upstream and downstream of Cle Elum Lake (Table 2). For this population, spawning and rearing habitat (SR habitat), if it is present at all, will be located upstream of Cle Elum Dam. FMO as well as juvenile rearing habitat is located in Cle Elum Lake. However, areas downstream of the dam in the Cle Elum River serve as FMO habitat for bull trout entrained out of Cle Elum Dam. There is also no SR habitat downstream of Cle Elum Dam.

Table 2. Habitat delineations for PCE analysis for those bull trout local populations affected by the proposed action.

Geographic Area Local Population Habitat Type within Action Area

Upper Yakima Adfluvial Populations Affected by Proposed Action

Cle Elum Lake Cle Elum and Waptus Lakes FMO & SR

Cle Elum River Cle Elum River FMO

The current condition of bull trout critical habitat within the Cle Elum watershed is classified as not properly functioning. This is generally due to blocked migratory corridors, loss of complex river habitat, altered channel and watershed conditions, and extreme hydrologic patterns. The condition of feeding, migratory, and overwintering habitat in the Yakima Core Area is at high risk (i.e., not properly functioning) for bull trout because of poor water quality, lack of adequate habitat complexity, poor channel complexity, degraded instream flow or hydrology, highly disturbed watershed conditions, and the widespread presence of brook trout.

For the purpose of this assessment, the Service recognizes that each PCE works in concert with others to support a designated use. Often, there is overlap between relevant factors for several PCEs. For example, PCEs 5 and 8 each consider water temperature, but in different ways. This section defines the individual bull trout PCEs and clarifies how the Service evaluated each. It should be noted that the analysis of PCEs for this consultation is limited to only those PCEs that are present within the action area and that could be directly or indirectly affected by the proposed action.

PCE 1: Springs, seeps, groundwater sources, and subsurface water connectivity (hyporheic flows) to contribute to water quality and quantity and provide thermal refugia.

PCE 1 plays different roles depending on the habitat type. In spawning and rearing habitats, groundwater influence can provide an important cue for spawning behaviors (75 FR 63898, page 63930, citing Baxter and Hauer 2000). In FMO habitat, groundwater can provide a source of thermal refugia and impact water quality. The importance of this contribution to FMO habitat is relative to other sources of thermal refugia and water quality.

What little functional flood plain that remains has been, and continues to be, affected by Reclamation Project operations. River operations for irrigation and flood control alter the natural hydrograph by impounding high flow events. A common effect of these operations is a sharp reduction in the frequency with which high flow events recharge the alluvial flood plain aquifer.

Truncation of flood peaks by capture in reservoirs also reduces the duration, magnitude, and spatial extent of flood plain inundation. This not only alters the quantity, quality, and timing of groundwater discharge to the river but also diminishes the availability, extent, and temporal duration of off-channel habitats. These changes in the pattern of floodplain inundation also have the undesirable effect of encouraging further commercial and residential development on the flood plain. Flood plain disconnection combined with flow regulation (i.e., the inversion and truncation of the natural hydrograph) have dramatically reduced river flood plain interactions.

The result has been a loss of horizontal and vertical connectivity, diminished habitat heterogeneity through the loss of off-channel habitat, and a general loss of ecosystem function.

Because these alterations are concentrated in the lower watershed, this PCE illustrates the general pattern described above of degraded conditions in the lower watershed and good conditions in the upper reaches of tributaries. Considering the scale of the entire subunit, we believe the baseline condition of this PCE is “not fully functioning.”

PCE 2: Migration habitats with minimal physical, biological, or water quality impediments between spawning, rearing, overwintering, and freshwater and marine foraging habitats, including but not limited to permanent, partial, intermittent, or seasonal barriers.

There are areas where impediments exist in the action area. To evaluate this PCE, the Service considered physical impediments including the presence of Cle Elum Dam. A recurrent effect on PCE 2 in reservoirs is associated with the exposure of the varial zone. Progressive drawdown of reservoirs leads to expansion of varial zones, which can present both passage challenges to migratory bull trout and increase predation risk, because tributary channels passing through varial zones often lack habitat complexity and cover. Varial zones can present impediments to bull trout migration in different ways. In some cases, varial zones can expose physical barriers as well.

Reservoir storage operations at Cle Elum Dam degrade bull trout habitat by impairing water quality, habitat access, habitat elements (e.g., substrate embeddedness in the varial zone), channel condition and dynamics, flow/hydrology, and watershed conditions (e.g., the disturbance regime). These impacts are most severe in the lower reaches of the Cle Elum River where it crosses the varial zone due to highly degraded habitat conditions created by drawdown operations (e.g., see Wissmar and Craig 2004, pages 25-26; Reclamation 2015a, page 325).

Under ongoing operations, habitat quality is degraded annually in the entire littoral zone of Cle Elum Reservoir and in the lower reaches of the Cle Elum River at all pool heights below full pool. Ongoing habitat impacts due to reservoir storage operations at Cle Elum Dam are likely to continue to impair the growth and survival of exposed bull trout and further reduce currently small local bull trout population sizes. This leads us to conclude the overall condition of this PCE in the action area to be “not fully functioning.”

PCE 3: An abundant food base, including terrestrial…