HAHD_RFP Attach 11 - NMFS 2019 BIOP.pdf

g3endllg Text Box Howard A. Hanson Dam - Fish Passage Facility 35% DDR ATR-BCOES Submittal g3endllg Text Box Attachment 11 g3endllg

NMFS 2019 Biological Opinion g3endllg

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WCR-2014-997

UNITED STATES DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

NATIONAL MARINE FISHERIES SERVICE

West Coast Region 1201 NE Lloyd Boulevard, Suite 1100 Portland, OR 97232

Refer to NMFS No.:

WCR-2014-997 February 15, 2019

Laura Boerner U.S. Army Corps of Engineers Seattle District Environmental and Cultural Resources Branch P.O. Box 3755 Seattle, Washington 98124-3755

Re: Biological Opinion on Howard Hanson Dam, Operations, and Maintenance, Green River

(HUC 17110013) King County, Washington

Dear Ms. Boerner:

Thank you for your February 14, 2018, letter and biological assessment (BA) (Corps 2014) requesting to reinitiate consultation with NOAA’s National Marine Fisheries Service (NMFS) pursuant to section 7 of the Endangered Species Act of 1973 (ESA) (16 U.S.C. 1531 et seq.) for the Howard Hanson Dam (HAHD) Project in King County, Washington.

NMFS’ final biological opinion pursuant to ESA section 7(a)(2) on the effects of the HAHD is enclosed with this letter. We shared a draft opinion with the Corps on October 27, 2015. In our final opinion we conclude that the proposed action is likely to jeopardize the continued existence of ESA-listed Puget Sound (PS) Chinook salmon, PS steelhead, and Southern Resident killer whales (SRKW), and that the proposed action is likely to result in the adverse modification of these three species’ critical habitat designated under the ESA. Our opinion includes a Reasonable and Prudent Alternative to the proposed action that, if implemented by the Corps, will offset the effects of the proposed action such that the effects are not likely to jeopardize these species or adversely modify their designated critical habitat.

We also evaluated potential impacts of the action on essential fish habitat (EFH) in accordance with section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and Management Act (MSA) (16 U.S.C. 1801 et seq.) and implementing regulations at 50 CFR 600. We conclude that the proposed action would adversely affect EFH designated for Pacific Coast Salmon.

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TABLE OF CONTENTS

1. INTRODUCTION

1.1 Background

1.2 Consultation History

1.3 Proposed Action

1.3.1 Flow Management Operations

1.3.1.1 Winter Flood Risk Management

1.3.1.2 Winter Non-Flood Reservoir Operations

1.3.1.3 Spring Reservoir Refill

1.3.1.4 Summer Conservation Flows

1.3.2 Section 1135 Ecosystem Restoration Project

1.3.3 Municipal and Industrial Water Storage

1.3.4 General Reservoir and Flow Management

1.3.5 Gravel Nourishment

1.3.6 Wood Debris Management

1.3.7 Reservoir Habitat Stewardship Activities

1.3.8 Other Activities

1.4 Action Area

2. ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL TAKE

STATEMENT

2.1 Analytical Approach

2.2 Range-Wide Status of the Species and Critical Habitat

2.2.1 Status of Species

2.2.1.1 Puget Sound Chinook Salmon

2.2.1.2 Puget Sound Steelhead

2.2.2 Status of Designated Critical Habitat

2.2.2.1 Rangewide Status of Critical Habitat for Puget Sound Chinook salmon and PS steelhead

2.2.3 Southern Resident Killer Whales

2.3 Environmental Baseline

2.3.1 Overview of the Environmental Baseline

2.3.2 Status of Fish Habitat in the Action Area

2.3.2.1 Water Quality

2.3.2.2. Coarse Sediment Supply

2.3.2.3 LWD Supply and Riparian Conditions

2.3.2.4 Instream Flows

2.3.2.5 Floodplain Connectivity

2.3.2.6 Aquatic Productivity

2.3.2.7 Lifestage Specific Habitat Conditions

2.3.3 Status of Southern Resident Killer Whale Habitat in the Action Area

2.3.3.1 Prey Availability

2.3.3.2 Contaminants

2.3.3.3 Vessel Activities and Sound

2.3.3.4 Non-Vessel Sound

2.3.4 Summary of Baseline Conditions for Southern Resident Killer Whales

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2.4 Effects of the Action on the Species and its Designated Critical Habitat

2.4.1 Method of Analysis

2.4.2 Analysis of Effects

2.4.2.1 Water Management Operations

2.4.2.2 Section 1135 Ecosystem Restoration Project

2.4.2.3 Municipal and Industrial Water Supply

2.4.2.4 General Reservoir and Flow Management

2.4.2.5 Water Quality

2.4.2.6 Deviation from Normal Operations

2.4.2.7 Gravel Nourishment

2.4.2.8 Woody Debris Management

2.4.2.9 Reservoir Habitat Stewardship Activities

2.4.3 Effects on Puget Sound Chinook salmon

2.4.3.1 Adult Migration Spawning and Incubation

2.4.3.2 Juvenile Rearing and Outmigration

2.4.3.3 Summary of effects on PS Chinook salmon

2.4.3.4 Puget Sound Chinook Salmon Designated Critical Habitat

2.4.3.5 Summary of Effects on PS Chinook Salmon Critical Habitat

2.4.4 Effects on Puget Sound Steelhead

2.4.4.1 Adult Migration, Spawning and Incubation

2.4.4.2 Juvenile Rearing and Outmigration

2.4.4.3 Summary of Effects on PS Steelhead

2.4.4.4 Puget Sound Steelhead Critical Habitat

2.4.4.5 Summary of Effects on PS Steelhead Critical Habitat

2.4.5 Southern Resident Killer Whales

2.5 Cumulative Effects

2.5.1 Puget Sound Chinook Salmon and Puget Sound Steelhead

2.5.1.1 Human Population Growth, Land Use, and Climate Change

2.5.1.2 Washington State

2.5.1.3 Tacoma’s Water Supply

2.5.1.4 Puget Sound Chinook Salmon Recovery Plan & the Shared Strategy for Puget Sound

2.5.2 Southern Resident Killer Whales

2.6 Integration and Synthesis

2.6.1 Puget Sound Chinook Salmon

2.6.2 Puget Sound Steelhead

2.6.3 Southern Resident Killer Whales

2.7 Conclusions

2.7.1 Puget Sound Chinook Salmon and Puget Sound Steelhead

2.7.2 Southern Resident Killer Whales

2.8 Reasonable and Prudent Alternative

2.8.1 RPA Action Item 1 – Permanent Downstream Fish Passage System

2.8.2 RPA Action Item 2 – Interim Actions

2.8.3 The Corps’ Implementation Decision

2.8.4 Analysis of the Effects of the Proposed Action As Modified by the RPAs

2.8.4.1 Effects of Permanent Downstream Fish Passage System

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2.8.4.2 Effects During the Interim Period and Redd Scour Reduction Proposed in RPA Action Item 2

2.8.4.3 Effects of the RPA on Southern Residents and Their Critical Habitat

2.8.4.4 Conclusions

2.9 Incidental Take Statement

2.9.1 Amount or Extent of Take

2.9.1.3 Incidental take during the operation, and monitoring of the permanent downstream fish passage system

2.9.2 Effect of the Take

2.9.3 Reasonable and Prudent Measures, and Terms and Conditions

2.10 Reinitiation of Consultation

3. MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT

ESSENTIAL FISH HABITAT CONSULTATION

3.1 Essential Fish Habitat Affected by the Project

3.2 Adverse Effects to Essential Fish Habitat

3.3 Essential Fish Habitat Conservation Recommendations

3.4 Statutory Response Requirement

3.5 Supplemental Consultation

4. DATA QUALITY ACT DOCUMENT & PRE-DISSEMINATION REVIEW

5. REFERENCES

APPENDIX A: Design Process and Criteria for the Green River Permanent Downstream Fish Passage System APPENDIX B: Best Management Practices for In-Water Work APPENDIX C: Performance Criteria for Howard Hanson Dam Permanent Downstream Fish Passage System (PDFPS) APPENDIX D: HAHD Interim RPA: Water Management Operations to Reduce Redd Scour – Monitoring and Adaptive Management

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ACRONYMS AND ABBREVIATIONS

ADP Adaptive Management Plan af Acre-feet (43,560 cubic feet) AWSP Additional Water Supply Project BA Biological Assessment

BMI Benthic Macroinvertebrates BRT Biological Review Team BMP Best Management Practice Corps US Army Corps of Engineers DBH Diameter at breast height DIP Demographically Independent Population DOE Department of Ecology DPS Distinct Population Segment DQA Data Quality Act EFH Essential Fish Habitat ESA Endangered Species Act ESU Evolutionarily Significant Unit GRFMCC Green River Flow Management Coordination Committee HAHD Howard A. Hanson Dam HMP Harvest Management Plan HSRG Hatchery Scientific Review Group HUC Hydrologic Unit Code ITS Incidental Take Statement LWD Large Woody Debris MIT Muckleshoot Indian Tribe MMD Mud Mountain Dam MPG Major Population Group MSA Magnuson-Stevens Fishery Conservation and Management Act MSY Maximum Sustainable Yield NOR Natural Origin Recruits NMFS National Marine Fisheries Service NTU Nephelometric Turbidity Unit Opinion Biological Opinion PBF Physical or Biological Features (characteristics of critical habitat) PCE Primary Constituent Element PDFPS Permanent Downstream Fish Passage System PFMC Pacific Fishery Management Council PIT Passive Integrated Transponder PS Puget Sound

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PSE Puget Sound Energy PSTRT Pacific Sound Technical Recovery Team RM River Mile RPA Reasonable and Prudent Alternative

RPM Reasonable and Prudent Measures Southern Resident Southern Resident Killer Whale

SSPS Shared Strategy for Puget Sound TPU Tacoma Public Utilities TRT Technical Recovery Team

TMDL Total Maximum Daily Load

USFWS U.S. Fish and Wildlife Service USGS U.S. Geologic Survey WDFW Washington Department of Fish and Wildlife

WDOE Washington Department of Ecology

VSP Viable Salmonid Population

WRIA Water Resource Inventory Area WWTIT Western Washington Treaty Indian Tribes

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1. INTRODUCTION

This Introduction section provides information relevant to the other sections of this document and is incorporated by reference into Sections 2 and 3 below.

1.1 Background

The biological opinion (Opinion) and incidental take statement (ITS) portions of this document were prepared by National Marine Fisheries Service ( NMFS) in accordance with the Endangered Species Act (ESA) of 1973, (16 U.S.C. 1531 et seq.), and implementing regulations at 50 CFR

402. Included in this Opinion is an analysis of the proposed action’s likely effects on recently designated critical habitat for Puget Sound steelhead.

NMFS also completed an Essential Fish Habitat (EFH) consultation in accordance with section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and Management Act (MSA) (16 U.S.C. 1801 1855(b)) and implementing regulations at 50 CFR 600.

This Opinion and EFH conservation recommendations are both in compliance with section 515 of the Treasury and General Government Appropriations Act of 2001 (Public Law 106-5444) (“Data Quality Act” (DQA)) and underwent pre-dissemination review.

This Opinion analyzes the U.S. Army Corps of Engineers’ (Corps’) proposed action to continue to operate and maintain its existing Howard A. Hanson Dam (HAHD). Understanding HAHD requires knowledge of other activities and facilities. Three and a half miles downstream from HAHD is Tacoma Water’s (Tacoma’s) Headworks Dam, built in 1913 (obstructing fish passage to the upper watershed) to divert water to supply the City of Tacoma, WA. The Corps subsequently developed HAHD in 1962 for the primary authorized purposes of flood control (now termed flood risk management) and the secondary purpose of fish conservation.

In April 1997, under Section 1135 of the 1986 Water Resources Development Act (WRDA), as amended, the U.S. Congress approved an ecosystem restoration project to augment summer low flows in the Green River to improve downstream fish habitat and fish survival by capturing more water during the spring at HAHD for release during the summer low flow period. The City of Tacoma was the local sponsor. The ecosystem restoration project included additional water storage of up to 5,000 acre-feet to augment low streamflows and a collection of habitat restoration projects around the reservoir. Rates of water capture and release were to be adaptively managed, depending on real-time ecosystem restoration needs.

In 1999, Congress authorized the HAHD Additional Water Storage Project (AWSP) which added water storage for Tacoma’s municipal water supply and ecosystem restoration as project purposes. The AWSP was adopted by Congress under the 1999 Federal Water Resources Development Act (WRDA, 1999; PL 106-53), which authorized the Corps to store an additional 20,000 acre-feet (af) of water behind HAHD to be subsequently released for Tacoma’s municipal and industrial (M&I) water use during the summer when natural flows are low and demand high.

The 1999 WRDA also authorized several ecosystem restoration projects, including construction of facilities to improve downstream fish passage at HAHD. The AWSP was designed to operate

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as a Federal project in which Tacoma was the local sponsor and shared a portion of the project costs.

The AWSP is a major component of Tacoma’s efforts to expand its water supply through its Second Supply Project. Tacoma has addressed the effects of its Green River operations, including the effects of its Second Supply Project (Tacoma’s interest that is served by the AWSP) in its July 2001 ESA Section 10(a)(1)(B) Habitat Conservation Plan (HCP) (Tacoma 2001). 1 The HCP includes: a commitment to maintaining minimum instream flows downstream from Headworks Dam, installing and operating an adult fish trap and haul system at Headworks Dam, screening to protect juvenile fish at Tacoma’s diversion, and numerous fish and wildlife habitat improvement measures upstream of HAHD where Tacoma owns about 11% of the upper Green River watershed. Most of the fish and wildlife habitat improvement projects are components of the AWSP and include a majority federal cost-share. The AWSP governs the operation, management, and long-term maintenance of these improvements. Tacoma has completed most fish protection elements of the HCP, including the upstream passage trap and haul system, but the facility has not yet been operated due to concerns that poor downstream passage survival through HAHD of the progeny produced would negate any potential benefits.

The background to this consultation is complex. The AWSP is a joint project between the Corps and Tacoma. However, as the Federal lead for the project, the Corps is responsible for conforming the project with the ESA. Federal entities are obligated to consult under section 7 of the ESA to ensure that their actions do not jeopardize the continued existence of ESA-listed species, or destroy or adversely modify their critical habitats. Non-federal entities may obtain an incidental take permit (ITP) to avoid potential take liability under the ESA for their activities, as has Tacoma. To be clear, the Second Supply Project is entirely a Tacoma project, while the AWSP is a Federal project for which Tacoma is the local sponsor.

In 2000, the Corps also consulted with NMFS on its proposed actions at HAHD, including the AWSP and a new downstream passage facility and temperature control structure at HAHD, and we concluded that the Corps’ proposed action in its 2000 BA (Corps 2000) would avoid jeopardy and destruction and adverse modification of critical habitat (NMFS 2000). In the current consultation, the Corps changed the suite of actions it proposed in 2000 by eliminating its proposal to install and operate a new downstream fish passage and temperature control facility at

HAHD.

Tacoma’s ITP and conservation measures adopted under the HCP are part of the environmental baseline, and the Corps’ actions, proposed in 2000 that have been completed are also part of the environmental baseline for this consultation.

This context is vital to understanding the overall effects of the continued operation and maintenance of HAHD. HAHD’s originally authorized purposes of flood risk management and

1 Tacoma’s HCP covers all aspects of Tacoma’s water supply project in the Green River basin. Reintroducing anadromous fish to the upper Green River watershed is a part of the HCP and the AWSP (Corps 1998), including an upstream fish passage system at Headworks dam, a system for collecting and safely passing outmigrating fish at HAHD, and screening to exclude juvenile fish from Tacoma’s diversion. Tacoma has completed the adult fish trap and haul system and the juvenile exclusion screening at its Headworks facility.

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fish conservation (via water storage and release) have been supplemented to provide water storage for Tacoma’s municipal supply and use (AWSP). As mentioned above, the capture and subsequent release of an additional 5,000 af of water for ecosystem restoration was authorized in 1997. Developing new facilities to provide downstream fish passage at HAHD and several fish habitat improvement measures were also authorized under the AWSP. The proposed action for this consultation does not include construction and operation of a juvenile fish collection and passage system at HAHD.

1.2 Consultation History

This Opinion is the result of the Corps reinitiating consultation on its Howard Hanson Dam (HAHD) Project in King County, Washington; and the proposed action includes project operation and maintenance, as described in the Corps’ biological assessment (BA) (Corps 2014). This Opinion supersedes the biological opinion issued for the continued operation and maintenance of Howard Hanson Dam NMFS issued October 20, 2000 (NMFS 2000).

The Corps’ initial consultation with NMFS on operation and maintenance of HAHD (NMFS 2000) followed the Corps’ Final Environmental Impact Statement (EIS) for the Additional Water Storage Project (AWSP) (Corps 1998). NMFS’ ESA Section 7(a)(2) consultation on issuance of an Incidental Take Permit (ITP) to Tacoma to implement its HCP (NMFS 2001) occurred after the 2000 HAHD biological opinion (NMFS 2000). Tacoma’s ITP application included measures aimed at mitigating the effects of its Second Supply Project.

In its initial consultation with NMFS on the operation and maintenance of its HAHD project in 2000, the Corps proposed to design, construct, and operate a juvenile downstream passage fishway and multi-level intake structure to control discharge water temperatures, along with a number of other fish habitat conservation measures. NMFS relied on the Corps’ commitment to construct and operate this new fishway and temperature control tower by a reasonable, but unspecified, date, along with the other aspects of the action proposed in 2000, and concluded that the proposed action would not jeopardize the continued existence of the species, or destroy or adversely modify their critical habitats (NMFS 2000). As of 2012, the Corps had not completed design of the downstream passage facility and multi-level intake system, and abandoned its commitment to construct them. As explained by Colonel Estok (Corps retired) in a September 2012 meeting with NMFS, that decision led the Corps to request re-initiation of consultation.

NMFS met with the Corps on October 9, December 10, 2012, and February 13, 2013 to discuss re-initiation of the HAHD consultation. NMFS held government to government meetings with the Muckleshoot Indian Tribe on June 20, 2013, and December 13 and 20, 2013, to discuss this consultation. NMFS and the Corps have met several more times since.

The Corps formally requested to reinitiate consultation on February 14, 2014 (Corps 2014).

NMFS received the supplemental BA at the same time.

The Corps’ proposed action for this consultation (Corps 2014) does not include developing a new passage system for downstream migrating juvenile salmon and steelhead or a multi-level

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intake system to control discharge water temperatures, and several other actions proposed in its 2000 BA (Corps 2014, Appendix A).

This biological opinion is based on information provided in NMFS’ 2000 biological opinion (NMFS 2000), the Corps’ new BA (2014), field investigations, and other sources of information listed in the references cited section of the opinion. A complete record of this consultation is on file at NMFS’ West Coast Regional Office in Portland, Oregon.

1.3 Proposed Action

“Action” means all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies (50 CFR 402.02). Interrelated actions are those that are part of a larger action and depend on that action for their justification. Interdependent actions are those that have no independent utility apart from the action under consideration (50 CFR 402.02). Under the proposed action, there are no proposed changes to any of the actions interrelated and interdependent to the proposed action. Additionally, the interrelated and interdependent actions to the proposed action have received prior ESA consultation (WSB-00-198) and are included in the Tacoma Water Habitat Conservation Plan (HCP) (WSB-00-522). Therefore, we consider interrelated and interdependent actions as part of the environmental baseline (Section 2.3) and not as part of the proposed action.

Interrelated/Interdependent actions include:

1. Withdrawal of the full 20,000 af of water at the Tacoma Headworks Dam for M&I use under the AWSP (WSB-00-198, WSB-00-522).

2. Upstream fish collection and transport facility at the Headworks Dam (WSB-00-198, WSB-00-522)

3. Downstream fish bypass facility at the Headworks Dam (WSB-00-198, WSB-00-522).

4. Integrated conservation measures (WSB-00-198, WSB-00-522).

Howard Hanson Dam is a rock and earthfill dam, authorized by the Rivers and Harbors Act (RHA) of 1950 and completed in 1962 for the purposes of flood risk management and providing fish conservation. Located at river-mile (RM) 64.5, the dam is 450 feet wide and 235 feet high from bedrock to crest. The project occupies 627 acres, with an additional 1,500 acres of easements for the reservoir, road access, and monitoring locations. Figure 1 shows the location of the dam. Figure 2 illustrates the vertical side profile of HAHD, noting key structural elements including the outlet tunnel, 48” bypass pipe, the spillway, and the dam crest. The elevations of various pool storage elevations are also shown.

Details of the proposed action are presented in the BA (Corps 2014) and we incorporate that description here by reference, and provide it below.

The Corps proposes to operate the project in perpetuity to provide: (1) flood-risk management of the Green River, (2) low-flow augmentation for fish conservation during the summer and fall, (3) ecosystem restoration, and (4) water supply for municipal and industrial (M&I) purposes. The Corps has operated the project to reduce flood risk and augment low-flows since the project was completed in 1962. Since 1998, the Corps has been implementing the Section 1135 ecosystem

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restoration project which added 5,000 acre-feet of water stored in HAHD to augment stream flows to protect steelhead redds from dewatering, improve juvenile salmonid summer rearing habitat conditions, and to improve spawning conditions for Chinook salmon. Ecosystem restoration projects of gravel and large wood nourishment downstream from the dam have been conducted by the Corps since 2003 and 2004 respectively.

Since 2007, the Corps has been storing water to 1,167 feet elevation during the spring annually to provide water fish conservation, flow augmentation, and M&I water for Tacoma. The Corps is currently capturing and storing 20,000 ac ft of water in the reservoir for later use during the spring, summer, and fall. The project is currently managed at the discretion of the Corps to ensure a net benefit to natural resources from storage of the AWSP water. The Corps considers that the water stored for M&I purposes to be relegated to a subordinate level of priority as compared to requirements imposed by natural resource concerns, in the event that conflict arises between these two considerations. Natural resource benefits are accrued under current operations by using at least 10,000 ac-ft (or 50%) of the stored M&I water for the benefit of natural resources in the form of flow augmentation to protect steelhead redds from dewatering, improve juvenile salmonid summer rearing habitat conditions, and to improve spawning conditions for Chinook salmon. Following implementation of Phase 1 of the AWSP, up to 20,000 af annually would be discharged from HAHD and it is anticipated that this entire volume would be diverted for M&I use at Tacoma’s Headworks Dam, although actual use of this Phase 1 water would be used at the discretion of Tacoma, consistent with the HCP.

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Figure 1. Howard Hanson Dam, reservoir, and vicinity. Source: Corps 2014.

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Figure 2. HAHD reservoir storage volumes and allocation. Source: Corps 2014.

1.3.1 Flow Management Operations

1.3.1.1 Winter Flood Risk Management

The project is authorized to provide maximum flood storage up to 106,000 acre-feet from November through February. However, the storage capacity has been reduced to about 104,000 acre-feet due to the accumulation of sediment in the reservoir since its construction in 1962 (Corps 2014). Figure 3 illustrates the minimum flood storage capacity that would be reserved in the reservoir throughout the year. The project regulates runoff from 46 percent of the total drainage area of the Green River. Flood events that require regulation are expected to have a 50 percent chance of occurrence each year (Corps 2011). Releases from the dam during a flood are made to avoid flow in excess of 12,000 cfs as measured at the U.S. Geological Survey (USGS) stream gage (USGS Station No. 12113000) at Auburn, WA (RM 32), which is the leveed channel capacity of the lower Green River. To provide a margin of safety against errors in forecasted local inflow (i.e., inflow downstream of HAHD), the project outflow would be regulated to a flow objective of 10,000 cfs at Auburn on the rising limb of a flood hydrograph.

The target flow at Auburn could be increased to 12,000 cfs during a flood recession (once the peak of uncontrolled inflows downstream of HAHD have passed) to evacuate stored flood water as rapidly as practicable.

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Figure 3. Minimum reservoir storage allocated for HAHD flood risk management. Source, Corps 2014

During a flood event, floodwaters would be stored in the reservoir and the maximum outlet tunnel discharge would generally be limited to 10,000 cfs. During extreme inflow events the spillway would be used to discharge water from the project in order to maintain adequate reservoir storage as needed to prevent overtopping of the dam. Under this scenario, it is likely that flows downstream from the dam would exceed 12,000 cfs at Auburn. The frequency of floods that would exceed this 12,000 cfs threshold is predicted to be 0.7 percent (about a one in 140-year annual chance flood) (Corps 2011). To date, the spillway has not been used. On rare occasions, it is possible that no flow would be discharged from the dam in order to maintain flows below 12,000 cfs at the Auburn stream gage. This would occur if the local inflow below the dam was forecasted to exceed 12,000 cfs. This situation has occurred once (in 2009) since HAHD operations were initiated in 1962.

The Corps would generally discharge any remaining pool of summer augmentation water in early to mid-November to facilitate winter flood storage unless drought conditions require holding storage longer to meet instream flow and/or M&I water requirements. Outside of flood events, the project would be held with no pool storage all winter so that the maximum potential storage volume would be available to store water from severe storm events.

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1.3.1.2 Winter Non-Flood Reservoir Operations

The pool would be held to a minimum level all winter (el 1,074 to 1,076) to accommodate flood events, or as may be needed to avoid discharging water with excessive turbidity. The low winter pool, referred to as the turbidity pool, is the lowest reservoir elevation that can be held without releasing fine sediments that have been deposited in the reservoir. To avoid excessive sediment accumulation that would reduce available flood storage capacity in the reservoir, the Corps would annually draft the reservoir to: (1) locate, to the extent possible, the precise elevation range of the turbidity pool, and (2) remove the veneer of fine sediment that has accumulated in the reservoir over the prior year particularly at the lower elevations (but above 1,074 ft.). During this sediment clearing operation the Corps would gradually lower the reservoir until a noticeable increase in discharge turbidity was observed (the Corps would attempt to keep outflow turbidity below about 30 nephelometric turbidity units (NTUs) throughout this operation, although short-term exceedances may occur).

The Corps also proposes to operate the project to maintain a 1,075-foot pool elevation for one to two weeks during the winter to conduct maintenance and inspections at the dam. The Corps would attempt to schedule this maintenance and inspection to coincide with relatively low and constant project inflows to facilitate maintaining a constant pool elevation.

1.3.1.3 Spring Reservoir Refill

Spring refill would begin after the major flood risk season, beginning no earlier than February 20 (Figure 3). A portion of incoming water would be stored for the originally authorized fish conservation purpose, Section 1135 ecosystem restoration, and M&I water for Tacoma. The flow capture and storage rate would range from 0 to more than 50% of inflow. The target date for reaching full storage is June 1, although it can extend into July, depending on hydrologic conditions. The timeframe for the start and end of the water capture period could also be modified. Storage would be adaptively managed by the Corps in consideration of the viewpoints expressed by the members of the Green River Flow Management Coordination Committee (GRFMCC), a stakeholder group consisting of resource agencies, tribes, and other interested parties that meets biweekly via conference call. Spring water storage would provide about 24,200 af for fish conservation, 5,000 af for ecosystem restoration, and 20,000 af for use by Tacoma for its municipal water supply and to meet the instream flow schedule established by its agreement with the Muckleshoot Indian Tribe (MIT) and included in its HCP.2 By storing a portion of inflowing water, project discharge would be less than inflow by an average of 266 cfs during this period (166 cfs for ecosystem restoration and 100 cfs for the AWSP). These are described in more detail in the environmental baseline because the Corps has been storing water for these purposes since 2007.

In the event the reservoir is not filled to 1,167 feet for a given year, stored water would be allocated based on the historical implementation dates for the various storage purposes with the earlier implemented project purposes receiving priority. The order of priority would therefore be

2 Tacoma’s commitments to maintaining the minimum instream flows adopted through settlement with the MIT, or through its HCP are not the responsibility of the Corps.

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flow augmentation for purposes of downstream fish conservation, flow augmentation in support of the Section 1135 ecosystem restoration project, and then M&I water supply.

1.3.1.4 Summer Conservation Flows

After reservoir refill is complete in the late spring, the Corps would generally pass inflow and maintain the full reservoir until water is needed from storage. Releasing stored water for flow augmentation to provide fish conservation would follow a reservoir guide curve that ensures sufficient water is reserved in the reservoir to achieve a minimum discharge of at least 110 cfs with a reliability of 98 percent as measured at the USGS stream gage at Palmer about 4 miles downstream of the dam. The 110 cfs flow target was developed in the 1950s as the minimum needed to meet the fish conservation purpose of the original project authorization. Minimum discharge from the dam would be based on the 110 cfs flow target plus 113 cfs or reservoir inflow (unless Tacoma requests less to augment storage for later use), whichever is least, for Tacoma’s first diversion water right claim (Corps 2011).

The purpose of the flow augmentation is to provide ‘for the preservation of fish life” as defined in the project authorization documents. Conservation water would be used to augment river flow to meet specific conservation objectives coordinated between the Corps and the GRFMCC via a biweekly conference call. Based on past operation of this program, flow augmentation water would typically be used to augment steelhead incubation in the early summer and adult Chinook salmon upstream migration and spawning in the late summer and early fall according to the decisions of the committee. The Corps, in agreement with Tacoma, releases sufficient water to meet Tacoma’s potable water needs and its commitment to minimum flows at Auburn (Tacoma 2001). If the full volume of intended storage is not achieved during the spring, then available water would be allocated by priority purpose, from highest to lowest, where the highest priority is fish conservation from the original RHA 1950 project authorization (24,200 af), then Sec.

1135 flow augmentation (5,000 af), and then M&I water supply for Tacoma (up to 20,000 af).

Under the proposed action, the Corps would release the water stored under the AWSP (above el 1147) at rates and times requested by Tacoma.

1.3.2 Section 1135 Ecosystem Restoration Project

Under the Section 1135 ecosystem restoration project, 5,000 acre feet of water would be stored during the spring refill as described above in section 1.3.1.3. Water stored during the spring refill between elevation 1,141 and 1,147 feet would be allocated to the ecosystem restoration program.

The 5,000 af of ecosystem restoration project water would be adaptively managed in accordance with the needs of a given year and in consideration of the opinions of the GRFMCC.

The GRFMCC has been dividing the Section 1135 water roughly equally between flow augmentation for steelhead incubation in June and July and Chinook salmon upstream migration and water temperature moderation in August and September. The committee has the discretion to allocate the water otherwise and could choose to do so in the future. It should be understood that 5,000 af is not a substantial amount of water for stream augmentation (1 af is about equal to one-half sfd [second foot day, i.e., 1 cfs for 24 hours]).

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The ecosystem restoration project also includes four habitat restoration projects.

1.3.3 Municipal and Industrial Water Storage

The Corps relies on Tacoma to track their own storage/capture requirements as the Corps is not a party to the Tacoma surface water permit. In the event sufficient time (100 days) has not elapsed and not all 20 kaf of water can be allocated to Tacoma M&I because it would violate Tacoma permit conditions, then this stored water would be allocated to fish conservation and used to augment flows for instream resources in consideration of the opinions of the GRFMCC.

The Corps would discharge M&I water at rates and times as requested by Tacoma to serve its water needs (typically between June and November 1) consistent with Tacoma’s HCP (Corps, 2014). All stored water would be released prior to the onset of the flood risk season, beginning around November 1 (see Section 1.3.1.1).

The purpose of the AWSP is to store water for Tacoma for M&I use. Water stored between reservoir elevation 1147’ and 1167’ is tied to the AWSP increment of total storage. Storage of this water is managed by agreement between the Corps and Tacoma. The reduction in spring flows downstream from HAHD caused by increasing spring storage was addressed by the Corps in its AWSP EIS (Corps 1998) by closely mimicking the natural hydrograph and engaging in adaptive management to spread out water capture over a longer timeframe and take advantage of storm events to least impact aquatic resources.

Currently, the Corps considers water stored under the AWSP for M&I purposes to be relegated to a subordinate level of priority as compared to requirements imposed by natural resource concerns (see Section 1.3.1.3 above), in the event that conflict arises between these two considerations. Natural resource benefits are accrued under current operations by using at least 10,000 af annually (or 50%) of the stored AWSP water for the benefit of natural resources in the form of flow augmentation to protect steelhead redds from dewatering, improve juvenile salmonid summer rearing habitat conditions, and to improve spawning conditions for Chinook salmon. 3 Currently, the release of this water is managed at the discretion of the Corps. It is NMFS understanding, per the Corps’ supplemental BA (COE, 2014) , that following completion of this consultation and construction of the fish passage at HAHD, the Corps will release the entire volume of water stored under Phase 1 of the AWSP (up to 20,000 af annually) available to Tacoma. For purposes of this consultation, NMFS assumes that the entire volume of AWSP water would be discharged from HAHD and diverted for M&I use at Tacoma’s Headworks Dam, although actual use of this Phase 1 water would be made at Tacoma’s discretion, and Tacoma will adhere to flow regimes consistent with the HCP.

As part of Phase 1 of the AWSP and our original consultation (NMFS 2000), the Corps has constructed a suite of habitat mitigation and restoration projects within the Green River watershed. Since these habitat projects have already been constructed, they are not part of the proposed action presented in this opinion (see Section 2.3, Environmental Baseline). However, the Corps proposes to develop an O&M manual for these habitat projects to ensure that the projects are sufficiently maintained to serve their purpose for the duration of the AWSP (which

3 See Corps 2014, pages 17-18.

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is 50 years) and consistent with the Project Cooperation Agreement between the Corps and Tacoma, the project Feasibility Report (Corps 1998), and other official project documents.

Because this manual does not now exist, it cannot be reviewed as part of this consultation. All habitat improvement measures that have been constructed are part of the environmental baseline and are expected to remain in good functioning condition throughout the life of the action. At AWSP project completion, maintenance of project features (offsite habitat improvements) would be turned over to Tacoma as described in the Project Cooperation Agreement and the O&M manual. The Corps would retain an oversight role to ensure the O&M manual is implemented.

We thus rely on the Corps’ commitment to maintain them in good functioning condition throughout the life of the action.

Another component of the AWSP includes management of the spring reservoir refill to maximize benefits to aquatic habitat and downstream fish. This management has generally been implemented with some modifications. A final component that is still on-going includes monitoring side channel and lateral habitat areas in the downstream river and potentially developing a set of guidelines to apply knowledge gained from the monitoring.

While the Corps’ supplemental BA contemplates providing additional storage for Tacoma under Phase 2 of the AWSP around 30 years from now, Phase 2 is not part of the proposed action for this consultation (Corps 2014).

1.3.4 General Reservoir and Flow Management

Normal reservoir operations HAHD would normally maintain a small reservoir year around (see the above mention of the turbidity pool). Discharge to the Green River would always be via gates, either the large radial gate that controls the 19’ outlet tunnel or the smaller gate that controls the 48” bypass pipe. The 48” pipe would be used during the lower flow summer period because it allows finer control.

Management of storage and discharge would be done manually by project staff during normal working hours, Monday through Friday, between 7:30 AM and 4:00 PM. The project would not be staffed outside these times except during flood conditions or when inflow and or reservoir conditions require a change to the gate setting.

Upramping The Corps proposes to manage the project so that the tailwater gage height does not rise any faster than 1 ft/hr, except during flood events. The reason for the upramp limit is to avoid creation of hazardous conditions to downstream river users. Upramping at this rate is not known to cause adverse effects to fish.

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Downramping The Corps proposes to avoid reducing project discharge (termed downramping) at rates that could strand fish downstream of HAHD by following WDFW’s downramping guidelines (Hunter 1992) to the extent practicable (Table 1). Rapid downramping rates dewater the river margins more rapidly than small fish, which use these shallow habitats, are able to follow the receding shoreline, causing stranding. The Washington downramping guidelines were developed to prevent stranding of fish on river banks of gravel and sand bars. However the downramping guidelines do not prevent fish from being stranded in potholes, which may later drain or warm up and cause fish mortality. The critical flow below which downramping guidelines would apply is 1,500 cfs. Above this flow level the river channel cross section is steep enough that gravel bar stranding does not usually occur.

Table 1. HAHD downramping guidelines. The guidelines apply to discharges less than

1,500 cfs as measured at USGS Station No. 12105900 immediately downstream from the dam. Source: Corps 2014.

Time Period Daylight Hours Night Time Hours

February 16 - May 31 0 in/hr 2 in/hr June 1 – October 31 1 in/hr 1 in/hr

November 1 – February 15 2 in/hr 2 in/hr

Deviation from normal operation Operations may deviate from normal for maintenance activities, inspections, and during monitoring or testing for fishery resources that might be performed by the Corps or other agencies. The Corps is occasionally requested to reduce river flow by law enforcement jurisdictions to aid in the search for river drowning victims. Deviations would be considered on a case-by-case basis, and any flow modifications would be coordinated with resource agencies.

1.3.5 Gravel Nourishment

HAHD greatly reduces downstream sediment movement. The Corps proposes to place up to 14,000 tons of spawning gravels, based on monitoring data and hydrologic conditions to ensure the project benefits salmonids. There are two designated deposition sites near RM 60, a short distance downstream of Tacoma’s Headworks Dam. The amount would be adaptively managed according to hydraulic conditions. The quantity, size gradation, and timing have been adjusted since 2003 to maximize spawning benefits and minimize adverse effects. The gravel would be placed on the site(s), typically in August but could also be placed during the winter months, and naturally occurring high winter stream flows would erode and distribute it downstream. The process would be managed to reduce the likelihood of creating waves of unstable gravel migrating downstream which could affect fish migration.

1.3.6 Wood Debris Management

The accumulation of wood behind HAHD is episodic and can range from hundreds of trees in large flood years to almost nothing in mild winters. Large woody debris (LWD) is defined as being greater than 12” in diameter and at least 20’ long, or any piece of wood containing a root

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ball greater than 4’ in diameter. Disposition of wood would be governed in part by an agreement between the Corps and Tacoma. In practice, the Corps would place as much large wood in the lower river as practical while avoiding creating a channel spanning logjam downstream of the nourishment site. Any remaining wood would be used for habitat purposes around the reservoir or for defined habitat restoration projects conducted by the Corps, Tacoma, or others. Tacoma’s HCP mirrors the Corps and Tacoma agreements regarding transport of 50% of large wood downstream, but also allocated the remaining reservoir wood among various habitat priorities and cultural uses by the Muckleshoot Indian Tribe (MIT). Because woody debris would be jointly managed by the Corps and Tacoma, wood could be used for all of the above described purposes depending on needs and wood availability.

LWD that is not immediately useful for habitat enhancement projects would be stored on site, or burned in accordance with the requirements of Puget Sound Clean Air Agency regulations if the accumulated debris posed a dam-safety threat (unlikely).

1.3.7 Reservoir Habitat Stewardship Activities

The Corps would conduct two habitat stewardship activities on the reservoir, the Baldi habitat boom to provide overhead cover in the reservoir and a loon nesting platform.

1.3.8 Other Activities

The Corps would continue to monitor project and environmental conditions at established monitoring sites in the basin and maintain project facilities. These include two meteorological stations, stream gages, water quality stations, and monitoring wells and piezometers for the purpose of monitoring water levels across the dam, and especially the right abutment. The Corps would perform regular facilities inspections and maintenance as needed, including mechanical equipment, debris and vegetation control, and maintenance of five miles of road at the project. It would also inspect and periodically repair the stilling basin, clean the trashrack, maintain tower gates, and rehab or replace stop logs. Specific action would be taken to stabilize the left bank slope downstream of HAHD by improving drainage and keeping the access road safe. The Corps proposes to employ best management practices (BMPs) as described in their BA for all maintenance activities.

1.4 Action Area

“Action area” means 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). The HAHD Project action area is the Green and Duwamish Rivers and their tributaries from the natural upstream limit of anadromous fish access (upstream of HAHD) downstream to Elliot Bay in Puget Sound, all project works, and all of Puget Sound (Figure 4). The proposed action would affect PS Chinook salmon and PS steelhead throughout the Green River watershed. The proposed action would affect Southern Residents in Puget Sound, the portion of their range that overlaps with substantial concentrations of PS Chinook, their preferred prey. The action area is also essential fish habitat (EFH) for Pacific salmon and groundfish.

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Figure 4. Green/Duwamish River basin and Puget Sound vicinity map.

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2. ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL

TAKE STATEMENT

The ESA establishes a national program for conserving threatened and endangered species of fish, wildlife, plants, and the habitat upon which they depend. As required by section 7(a)(2) of the ESA, Federal agencies must ensure that their actions are not likely to jeopardize the continued existence of endangered or threatened species, or adversely modify or destroy their designated critical habitat. Per the requirements of the ESA, Federal action agencies consult with NMFS and section 7(b)(3) requires that, at the conclusion of consultation, NMFS provides an opinion stating how the agency’s actions would affect listed species and their critical habitat. If incidental take is expected, section 7(b)(4) requires NMFS to provide an incidental take statement (ITS) that specifies the impact of any incidental taking and includes non-discretionary reasonable and prudent measures and terms and conditions to minimize such impacts.

2.1 Analytical Approach

This biological opinion includes both a jeopardy analysis and an adverse modification analysis.

The jeopardy analysis relies upon the regulatory definition of “to jeopardize the continued existence of a listed species,” which is “to engage in an action that would be expected, directly or indirectly, to reduce appreciably the likelihood of both the survival and recovery of a listed species in the wild by reducing the reproduction, numbers, or distribution of that species” (50 CFR 402.02). Therefore, the jeopardy analysis considers both survival and recovery of the species.

The adverse modification analysis considers the impacts of the Federal action on the conservation value of designated critical habitat. This biological opinion relies on the definition of "destruction or adverse modification", which “means a direct or indirect alteration that appreciably diminishes the value of critical habitat for the conservation of a listed species. Such alterations may include, but are not limited to, those that alter the physical or biological features essential to the conservation of a species or that preclude or significantly delay development of such features” (81 FR 7214).

The designation(s) of critical habitat for PS Chinook salmon used the term ‘primary constituent elements’ (PCEs) or ‘essential features’. The new critical habitat regulations (81 FR 7214) replace this term with ‘physical or biological features (PBFs). The shift in terminology does not change the approach used in conducting a ‘destruction or adverse modification’ analysis, which is the same regardless of whether the original designation identified primary constituent elements, physical or biological features, or essential features. In this biological opinion, we use the term physical or biological features (PBFs) in lieu of PCEs or essential features, as appropriate for the specific critical habitat.

We use the following approach to determine whether a proposed action is likely to jeopardize listed species or destroy or adversely modify critical habitat:

• Identify the rangewide status of the species and critical habitat likely to be adversely affected by the proposed action.

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• Describe the environmental baseline in the action area.

• Analyze the effects of the proposed action on both species and their habitat using an

“exposure-response-risk” approach.

• Describe any cumulative effects in the action area.

• Integrate and synthesize the above factors to assess the risk that the proposed action poses to species and critical habitat.

• Reach jeopardy and adverse modification conclusions.

• If necessary, define a reasonable and prudent alternative to the proposed action.

2.2 Range-Wide Status of the Species and Critical Habitat

This opinion examines the status of each species that would be adversely affected by the proposed action.