NMFS BO 12-3-2020.pdf

UNITED STATES DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

NATIONAL MARINE FISHERIES SERVICE

West Coast Region 1201 NE Lloyd Boulevard, Suite 1100

PORTLAND, OREGON 97232-1274

https://doi.org/10.25923/3zen-t721

Refer to NMFS No: WCRO-2018-00274 December 3, 2020

Lt. Col. Richard T. Childers U.S. Army Corps of Engineers Walla Walla District 201 North Third Avenue Walla Walla, Washington 99362-1876

Re: Endangered Species Act Section 7(a)(2) Biological Opinion for the Operation and

Maintenance of the Mill Creek Flood Control Project, Lower Mill Creek Subwatershed (170701020204), Middle Mill Creek Subwatershed (170701020202), Russell Creek Subwatershed (170701020801), Walla Walla County, Washington.

Dear Lieutenant Colonel Childers:

Thank you for your letter of September 26, 2018, requesting initiation of 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 Operation and Maintenance of the Mill Creek Flood Control Project. This consultation was conducted in accordance with the 2019 revised regulations that implement section 7 of the ESA (50 CFR 402, 84 FR 45016).

Thank you, also, for your request for consultation pursuant to the essential fish habitat (EFH) provisions in Section 305(b) of the Magnuson-Stevens Fishery Conservation and Management Act (16 U.S.C. 1855(b)) for this action. However, after reviewing the proposed action, we have determined that EFH is not in the action area. Therefore, EFH consultation is not necessary.

The enclosed document contains a biological Opinion (Opinion) prepared by NMFS on the effects of the Operation and Maintenance of the Mill Creek Flood Control Project (Project) in Walla Walla, Washington as proposed by the Walla Walla District, U.S. Army Corps of Engineers (Corps). This Opinion is based on the information provided in the December 2018 Biological Assessment (BA), numerous meetings, phone calls, emails, and letters exchanged on the proposed action. We shared draft sections of the Opinion with the Corps in December 2019.

A complete docket of this consultation is on file at the National Marine Fisheries Service’s Interior Columbia Basin Branch Office in Ellensburg, Washington.

In our final Opinion, we conclude that the proposed action is not likely to jeopardize the continued existence of ESA-listed Middle Columbia River (MCR) steelhead and is not likely to result in the adverse modification of this species’ critical habitat designated under the ESA.

As required by section 7 of the ESA, NMFS provided an incidental take statement (ITS) with this Opinion. The ITS includes reasonable and prudent measures (RPMs) that NMFS considers necessary or appropriate to minimize incidental take associated with the proposed action. The take statement sets forth nondiscretionary terms and conditions, including reporting requirements that the Corps and any person who performs the action must comply with to carry out the RPMs.

Incidental take from the proposed action that meets these terms and conditions will be exempt from the ESA take prohibition.

Please send comments to Colleen Fagan, Ellensburg Field Office, at colleen.fagan@noaa.gov.

She is also available at 541-786-8953 if you have questions or would like additional information regarding this ESA consultation.

Sincerely, Michael Tehan Assistant Regional Administrator

Enclosure cc: [File] Michael Erickson: Michael.Erickson@usace.army.mil Ben Tice: Ben.J.Tice@usace.army.mil Michelle Eames: michelle_eames@fws.gov Gary James: GaryJames@ctuir.org mailto:colleen.fagan@noaa.gov mailto:Michael.Erickson@usace.army.mil mailto:Ben.J.Tice@usace.army.mil mailto:michelle_eames@fws.gov

Endangered Species Act (ESA) Section 7(a)(2) Biological Opinion for the Operation and Maintenance of the Mill Creek Flood Control Project Mill Creek, Lower Mill Creek Subwatershed (170701020204), Middle Mill Creek Subwatershed (170701020202), Russell

Creek Subwatershed (170701020801), Walla Walla County, Washington

NMFS Consultation Number: WCRO-2018-00274

Action Agency: U.S. Army Corps of Engineers, Walla Walla District

Affected Species and NMFS’ Determinations:

ESA-Listed Species

Status Is Action Likely to Adversely Affect Species?

Is Action Likely To Jeopardize the Species?

Is Action Likely to Adversely Affect Critical Habitat?

Is Action Likely To Destroy or Adversely Modify Critical Habitat?

Middle Columbia River steelhead (Oncorhynchus mykiss)

Threatened Yes No Yes No

Consultation Conducted By: National Marine Fisheries Service, West Coast Region

Issued By: Michael Tehan Assistant Regional Administrator

Date: December 3, 2020 i

TABLE OF CONTENTS

TABLE OF CONTENTS .............................................................................................................. I

ABBREVIATIONS AND ACRONYMS ................................................................................... III

LIST OF FIGURES ..................................................................................................................... V

LIST OF TABLES ...................................................................................................................... VI

1. INTRODUCTION

1.1 BACKGROUND

1.2 CONSULTATION HISTORY

1.3 PROPOSED FEDERAL ACTION

1.3.1 Operations of the Structural Components of the Mill Creek Flood Control Project

1.3.2 Project Maintenance and Future Construction

1.3.3 Summary of Conservation Measures

2. ENDANGERED SPECIES ACT: OPINION AND INCIDENTAL TAKE STATEMENT

2.1 ANALYTICAL APPROACH

2.2 RANGEWIDE STATUS OF THE SPECIES AND CRITICAL HABITAT

2.2.1 Status of Middle Columbia River Steelhead

2.2.2 Status of Critical Habitat

2.3 ACTION AREA

2.4 ENVIRONMENTAL BASELINE

2.5 EFFECTS OF THE ACTION

2.5.1 Approach to the Analysis and Factors Considered

2.5.2 Effects on Fish

2.5.3. Effects on Critical Habitat

2.6 CUMULATIVE EFFECTS

2.6.1 Habitat Improvement

2.6.2 Chinook Salmon Reintroduction

2.6.3 Continued Development

2.6.4 Continued Use of Mill Creek Water for Municipal Water

2.7. INTEGRATION AND SYNTHESIS

2.8 CONCLUSION

2.9 INCIDENTAL TAKE STATEMENT

2.9.1 Amount or Extent of Take

2.9.2 Effect of the Take

2.9.3. Reasonable and Prudent Measures

2.9.4 Terms and Conditions

2.10. CONSERVATION RECOMMENDATIONS

2.11. REINITIATION OF CONSULTATION

3. DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW

ii

3.1 UTILITY

3.2 INTEGRITY

3.3 OBJECTIVITY

4. REFERENCES

iii

ABBREVIATIONS AND ACRONYMS

BA Biological Assessment BMP Best Management Practice BPA Bonneville Power Administration CFR Code of Federal Regulations cfs cubic foot per second CHART Critical habitat analytical review team Corps U.S. Army Corps of Engineers CMA Calcium-Magnesium Acetate CTUIR Confederated Tribes of the Umatilla Reservation DBH Diameter at Breast Height DPS Distinct Population Segment DQA Data Quality Act EFH Essential Fish Habitat EPA Environmental Protection Agency ESA Endangered Species Act ESU Ecologically Significant Unit FPP Mill Creek Fish Passage Plan FPRP (III) Corps Fish Passage and Restoration Actions in Washington State FR Federal Regulations FWS Fish and Wildlife Service FY Fiscal Year HUC Hydrologic Unit Code ICTRT Interior Columbia Technical Recovery Team IPCC Intergovernmental Panel on Climate Change ISAB Independent Scientific Advisory Board ITS Incidental Take Statement Manual Mill Creek Water Control Manual MCR Middle Columbia River MCFCZD Mill Creek Flood Control Zone District MCWG Mill Creek Work Group MOU Memorandum of Understanding MPG Major Population Group Msa Major Spawning Aggregations MSA Minor Spawning Aggregations msl Mean sea level NMFS National Marine Fisheries Service NEPA National Environmental Policy Act ODEQ Oregon Department of Environmental Quality OHWL Ordinary High Water Line OHLM Ordinary High Water Mark O&M Operation and Maintenance Opinion biological Opinion PBF Physical or Biological Feature PCE Primary Constituent Element iv

PIT Passive Integrated Transponder PL Public Law Project Mill Creek Flood Control Project PTAGIS PIT Tag Information System PTAGIS) RM River Mile RPA Reasonable and Prudent Alternative RPM Reasonable and Prudent Measure SEIS Supplemental Environmental Impact Statement SR Snake River SRFB Salmon Recovery Funding Board (Washington State) SRSRB Snake River Salmon Recovery Board T&C Terms and Conditions TMDL Total Maximum Daily Load UCR Upper Columbia River USC United States Code USFWS U.S. Fish and Wildlife Service USGS U. S. Geologic Survey VSP Viable Salmonid Population WDFW Washington State Department of Fisheries and Wildlife WDOE Washington State Department of Ecology WWCD Walla Walla Conservation District WWWBP Walla Walla Watershed Management Partnership v

LIST OF FIGURES

Figure 1. Diagram of the federally owned portion of the Project. Numbers in the diagram correspond to sections in Chapter 1 of the 2018 BA, the shaded area is owned by the Corps. Mill Creek flows from right to left in the diagram (Corps 2018a)

Figure 2. Middle Columbia River Steelhead DPS and Major Population Groups (NMFS 2009)

Figure 3. Natural and hatchery-origin escapement for the Walla Walla river population of summer steelhead (WDFW 2020a)

Figure 4. Timing and total number of days by month that unscreened flows have been diverted into Bennington Reservoir between 1945 and March 2020 and timing of juvenile and adult steelhead observations at the Mill Creek Diversion Dam, Nursery Bridge Dam video monitoring and CTUIR PIT Tag monitoring

Figure 5. The number of juveniles captured and tagged in the CTUIR operated Mill Creek smolt trap by day from 2003 through 2019

Figure 6. The total number of days by month (1981-2019) that the existing fish ladder was closed when flows reached 400 cfs (solid bars) compared to a future ladder that can pass 800 cfs (striped bars) over the same time period overlayed with steelhead presence

Figure 7. Hierarchical levels of salmonid species structure as defined by the ICTRTs for ESU/DPS recovery planning (NMFS 2009). In the figure above, the Walla Walla River MCR steelhead are an Independent Population and the Mill Creek population is a subset or subpopulation of the Walla Walla River population (as are the North and South Forks of the Walla Walla River) vi

LIST OF TABLES

Table 1. Actions that the Corps will implement beginning in FY 2020 to remove passage barriers on the federal section of the Project (Corps 2018b)

Table 2 Maintenance Actions at the Mill Creek Diversion Dam Requiring the Forebay to Be Lowered (From table A-2 in 2018 BA Appendix A)

Table 3. Major and minor spawning aggregations within the Walla Walla River portion of the Umatilla /Walla Walla MPG (SRSRB 2011)

Table 4. Population-level status by MPG for MCR steelhead (NMFS 2016). Comparison of updated status summary versus recovery plan viability objectives. Key: up arrow = improved since 2010 review, down arrow = decreased since 2010 review, oval = no change (adapted from NWFSC 2015). The arrows do not apply to the 2019 values. . 33

Table 5. Types of sites and essential physical and biological features designated as PBFs for MCR steelhead

Table 6. Number of miles of PBFs for MCR steelhead in the Mill Creek and Cottonwood Creek fifth-field watersheds (adapted from NMFS 2005b, Table J1)

Table 7. Normal precipitation for Walla Walla County, Washington

Table 8. Walla Walla River mean monthly flows (cfs) 1951–2019 and average monthly water temperatures (º F) (2002–2005) in the Walla Walla River measured at RM 18.2

Table 9. Mill Creek mean monthly flows (cfs) 1998–2019 measured at RM 12.6, approximately one mile upstream of Mill Creek Diversion Dam but downstream of some irrigation diversions

Table 10. The frequency and duration of flood events resulting in unscreened diversions of Mill Creek into Bennington Reservoir since 1945 (Adapted from Table 2-1 in (Corps 2018c) with most recent 2018-2020 information provided via email by B.Tice on March 23, 2020)

Table 11. Mill Creek Flow and Average Recurrence Interval Flow (cfs) (Corps 2018b)

Table 12. Proportion of average annual adult steelhead returns (175 fish) likely to be present in the federal footprint of the Project by month

Table 13. Proportion of average annual smolt production (7,614 smolts) present in the federal footprint of the Project by month vii

Table 14. The expected number of juveniles and adults diverted with the excess flow during a 24-hour diversion of the historic average depending on the month that the diversion occurs, 18 percent of the flow in January and February,16 percent in December, 22 percent in April, and 3 percent in November. We assume the average number of adults per month are evenly distributed across the month, and the diversion occurs on the date when the greatest number of juveniles have been observed based on smolt traps 2003-2019

Table 15. The number of days per month that upstream passage was unavailable 1981-2020 under current conditions of 400 cfs and proposed 800 cfs by 2025. The number of ladder closures per month, average length of closure, average return interval and probability of occurrence

Table 16. Numbers and sizes of O. mykiss salvaged in Mill Creek downstream of the Division Dam on June 29 and 30, 2004. The preceding week water temperatures in some parts of the stabilized channel had been at 88°F(Mendel 2004)

Table 17. Physical and biological features of critical habitat designated for ESA-listed species considered in this Opinion and corresponding species life history events

Table 18. Number of miles of PBFs for MCR steelhead in the Mill Creek and Cottonwood Creek fifth-field watersheds (NMFS 2005a)

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 National Marine Fisheries Service (NMFS) prepared this Opinion and incidental take statement (ITS) portions of this document in accordance with section 7(b) of the Endangered Species Act (ESA) of 1973 (16 USC 1531 et seq.), and implementing regulations at 50 CFR 402.

We completed pre-dissemination review of this document using standards for utility, integrity, and objectivity in compliance with applicable guidelines issued under the Data Quality Act (section 515 of the Treasury and General Government Appropriations Act for Fiscal Year 2001, Public Law 106-554). The document will be available within two weeks at the NOAA Library Institutional Repository [https://repository.library.noaa.gov/welcome]. A complete record of this consultation is on file at the Columbia Basin Branch Office in Ellensburg, Washington.

This Opinion analyzes the U.S. Army Corps of Engineers (Corps) proposed action to continue the operation and maintenance (O&M) of the Mill Creek Flood Control Project (Project) (Corps 2018a). Congress authorized the Project in 1938 and construction was completed in 1942. At that time, the Project consisted of the Mill Creek Diversion Dam; the off-stream reservoir, Bennington Reservoir; and the first division works, which was designed to distribute some of the excess flow into Yellowhawk and Garrison Creeks. There were no fish ladders until 1982. The Project is located between river mile (RM) 4.8 and 11.5 on Mill Creek in and near the City of Walla Walla, Washington. Mill Creek is a tributary to the Walla Walla River at RM 33.5, which in turn enters the Columbia River at RM 315 (ten miles downstream of the Columbia River junction with the Snake River). The proposed action will occur within the geographic range and critical habitat of the Middle Columbia River (MCR) steelhead (Oncorhynchus mykiss) Distinct Population Segment (DPS), which is listed as threatened under the ESA. The affected steelhead are part of the Umatilla/Walla Walla Major Population Group (MPG) and the Walla Walla population.

The Project is divided into two sections; the lower approximately six miles (RM 4.5 to approximately RM 10.4) is owned and managed by the local Mill Creek Flood Control Zone District (MCFCZD) and the upper approximately one mile (RM 10.4 to RM 11.5) is owned and operated by the Corps. This consultation analyzes the effects of the O&M actions taken by the Corps on the federally-owned section of the Project (also referred to as the federal footprint), from approximately RM 10.4 to RM 11.5, but does not include the actions taken by the local district on the locally managed section (Corps 2018a).

The federal footprint of the Project includes all structures associated with Mill Creek from approximately RM 10.4 to RM 11.5: two mainstem dams and forebay; a storage reservoir; the modified channel, levees, flood diversion canals, gates, and screens; the first 500 feet of distributaries Yellowhawk and Garrison Creeks (originating at RM 10.5); and 556 acres of https://repository.library.noaa.gov/welcome nearby land and open water. A detailed description of all the structures owned, operated and maintained by the Corps within the federal footprint of the Project is in the Biological Assessment (BA) (Corp 2018a) and below in section 1.3 of the proposed action.

The Corps owns, operates and maintains the major structures that control the Project, which includes elements that adversely affect ESA-listed salmonids and their habitats. Among other things described in more detail below, the Corps actions include:

1. Diverting flows at recurrence intervals of once every four years at the Mill Creek Diversion Dam, thus potentially diverting adult and juvenile MCR steelhead into Bennington Reservoir from which there is no egress.

2. Diverting flow from Mill Creek into Yellowhawk Creek under a Memorandum of

Understanding (MOU) with the Washington Department of Ecology (WDOE) to provide irrigation water and maintain fish habitat.

3. Management of two fish ladders within the Project that do not meet NMFS passage criteria due to delaying or obstructing passage at a wide range of flows.

4. Cleaning and maintenance of all the structures and areas within the federal footprint of the Project, which requires periodic fish salvage, passage blockage, dredging, and vegetation management including tree removal.

The background to this consultation is lengthy and complex. After 16 adult MCR steelhead were found dead at the base of Mill Creek Diversion Dam in 2002, the Corps provided NMFS with a BA (2003) and a request for consultation. In its initial consultation with NMFS on the O&M of the Project in 2003, the Corps proposed to design, construct, and operate a low-flow channel from RM 10.4 to 11.5 and construct new fish ladders at Mill Creek Diversion Dam (RM 11.5) and the Division Dam (RM 10.4). Initially, NMFS relied on the Corps’ commitment to construct and operate these new ladders but over the course of the consultation, the Corps was unable to offer a reasonable date for completion of the proposed actions included in the consultation.

Therefore, in September 2011, NMFS issued an Opinion (NWR-2003-00309) that concluded that the O&M of the Project was likely to jeopardize the continued existence of MCR steelhead and result in the destruction or adverse modification of designated critical habitat for MCR steelhead (described more fully below). The 2011 Opinion included a Reasonable and Prudent Alternative (RPA) with five elements that specified the following actions were required to avoid jeopardizing MCR steelhead:

1. The Corps will develop and implement an interim vegetation variance that promotes the development of riparian vegetation in the forebay and on the levees. The Corp will also develop and implement a plan to redesign the existing levee structures to include planting benches, overbuilt levee prism, or levee setback areas where riparian vegetation can develop.

2. The Corps will work with the local flood zone district, local governments and other stakeholders to implement levee management consistent with the habitat and water quality requirements of MCR steelhead.

3. Design and construct a low-flow channel within the federal footprint, and two new fish ladders, one at Mill Creek Diversion Dam and one at the Division Dam and,

4. The Corps will be responsible for coordinating efforts to salvage fish in the Mill Creek channel downstream of the Division Dam when flows become too low for fish to pass over the sills and move out of declining habitat.

5. Decrease the frequency of flood control diversions into Bennington Reservoir (the flood trigger) by only providing protection from events exceeding 3,500 cubic feet per second (cfs), which is the channel capacity.

The RPA included a deadline of 2015. The Corps responded that RPA Elements 2 and 4 were outside their authority or jurisdiction and would not be considered. The 2011 Opinion also described two RPMs with associated Terms and Conditions (T&Cs) including annual reporting requirements.

In February 2012, the Corp responded that the “analysis in the [Opinion] contained activities outside the [Corps] authority and jurisdiction.” In addition, the Corps responded to the RPA as follows:

1. RPA Element 1 the Corps would “revisit the vegetation variance issue under rules that are currently being developed by the Corp HQ”.

2. RPA Element 2 the Corps believed “addresses effects that are not part of the federal action, and are not within the action area. Therefore, this RPA Element …cannot be implemented consistent with the scope of the action agency’s legal authority and jurisdiction and it does not help avoid the likelihood of jeopardy or adverse modification associated with the proposed action.”

3. RPA Element 3 “The Corps intends to construct a low-flow channel and modify/replace fish passage structures at the first division works and Mill Creek Diversion Dam …design for the modification of the fish ladder at the first division [dam] is nearly complete, with construction scheduled in 2012 or 2013, subject to availability of funds.

4. RPA Element 4 “the [Corps] lacks authority to engage in off-project salvage efforts downstream of the [Division Dam].’

5. RPA Element 5 “The Corps has developed criterion, based on the results of the Flood Plain Study, for starting diversions at 2,400 cfs up to 3,500 cfs… The new diversion criteria should reduce adverse effects, and meet NMFS intent in RPA Element 5…”

In February 2015, with only the flood diversion trigger of 2,400 cfs considered to be meeting the RPA’s and no evidence of compliance with the other elements of the RPA or the T&Cs, the Corps reinitiated consultation for the O&M of the Project. During the course of the consultation the Corps changed the proposed action including reversing the flood diversion criterion back to 1,400 cfs and then withdrew the ongoing consultation until a new BA was prepared with the revised action. In March 2017, the Corps announced that the flood diversion criteria would change to 1,700 cfs and that is where it has remained since that time (there was no discussion with NMFS or USFWS regarding this change). NMFS received a new BA and request for consultation in September, 2018, as described below in 1.2 Consultation History.

The following authorities govern the current and proposed federal actions to operate and maintain the Project: (1) Section 4 of the Flood Control Act of 1938 (P.L. 75-761)1; (2) Flood Control Act of 1941 (P.L. 77-228); (3) Fish and Wildlife Coordination Act of 1958 (P.L. 85- 624)2; (4) Federal Water Protection Act of 1965 (P.L. 89-072); and (5) the Water Resources Development Act of 1976 (P.L. 94-587).3

1.2 Consultation History

On September 26, 2018, the Corps submitted a new BA and request for formal consultation on the O&M of the Project.

NMFS requested additional information from the Corps on October 31, 2018, for proposed actions included in the BA that will be completed “when funding is provided.” Specifically, NMFS requested that the Corps provide a timeline and reporting framework on the Corps’ efforts to acquire the funding needed to complete these actions.

NMFS received the Corps’ response on December 3, 2018, which included a timeline for future actions to be included as part of the proposed action. In the Corps response, they proposed construction of a new fish ladder at the Division Dam in 2020, completing the Mill Creek Diversion Dam fish ladder design in 2019 and construction by 2022. In September 2019, they revised the timeline for the design of the Mill Creek Diversion Dam date to fiscal year (FY) 2023 and construction date to fiscal year (FY) 2025 and construction of the low-flow channel by FY 2030, subject to availability of funding. Beginning in March 2019, the Corps, NMFS, and U.S.

Fish and Wildlife Service (USFWS) held frequent conference calls to clarify the proposed action.

NMFS shared several versions of the proposed action with the Corps and received a revision to the Project on January 16, 2020.

On May 31, 2019, the Corps requested to review a draft of the entire Opinion. NMFS offered to send sections as they were completed and the Corps declined, insisting that they wanted to see the entire draft, not sections. NMFS informed the Corps that sharing an entire draft would add a great deal of time, as a complete draft would require extensive internal review before sharing.

The Corps responded that they understood and still wanted to review an entire draft.

On a September 5, 2019, conference call, the Corps stated that they moved the timeline for completing a design and cost estimate for a selected alternative for the Mill Creek Diversion Dam fish ladder from FY 2019 to FY 2023 with a “best-case scenario” of construction in FY

1 Mill Creek Dam and Project works were authorized by the Flood Control Act of 1938, Public Law 761, 75th Congress, 28 June 1938 and Flood Control Act of 1941, Public Law 228 (Amendatory, 77th Congress, 18 August 1941.

2 Fish and Wildlife Conservation became a Project purpose when the Fish and Wildlife Coordination Act of 1958 was signed into law.

3 The Federal Water Protection Act of 1965, as amended, established recreational potential at the Project as a full Project purpose.

2025. The Corps also requested that the duration of the proposed action considered in this Opinion be 10 years.

On October 30, 2019, the Corps sent a follow-up email stating that the soonest there would be funding available to complete the design on the Mill Creek Diversion Dam fish ladder is by the end of FY 2023.

On December 5, 2019, NMFS held a conference call with the Corps to discuss certain elements of the Project and we also shared a part of the Effects Section of the draft Opinion. During the call, NMFS reviewed the parts of the Proposed Action that the Corps agreed to act on in 2011 but has not yet implemented. NMFS again requested an updated timeline for completion of the projects the Corps has included as part of the Proposed Action but for which there is not currently a design or funding. The Corps did not respond to our request.

On December 10, 2019, the Corps requested that NMFS share parts of the draft Opinion. NMFS agreed and sent the Proposed Action and the Environmental Baseline on December 12, 2019.

On January 16, 2020, the Corps changed the proposed action by modifying the flood diversion criterion as is described in the following section. NMFS initiated consultation on January 29, 2020, after receipt of additional information.

1.3 Proposed Federal 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).

The actions considered as part of the proposed action4 include: (1) Operation of the Project (Figure 1) under its current structural configuration: (2) Short-term and long-term actions that the Corps will implement beginning in FY 2020 regarding removal of passage barriers: (3) Changes in the operation after structural modifications are completed and: (4) Current and future maintenance of the federally-owned portion of the Project (Corps 2018a; 2018b; 2018c).

A full list of actions, including those actions the Corps deemed to be No Effect can be found in Appendix B of the BA (Corps 2018a). The full list of individual O&M actions (primarily maintenance) are not restated here; rather those parts of the proposed action that are relevant to understand the proposed action’s effects on MCR steelhead are described below.

This Opinion is based on information provided in NMFS’ 2011 Opinion (NMFS 2011b), the proposed action as described in the Corps’ BA including Appendices A and B (2018a), and Alternative 7 and Appendix A of the Corps Draft Supplemental Environmental Impact Statement (SEIS) (2018b; 2018c). Additional information was provided by field investigations, numerous telephone and email conversations and other sources of information listed in the references cited section of this Opinion. The proposed action includes all of the current operations and

4 The various structures that comprise the Project as well as the past operation and maintenance of those structures are not part of the proposed action, instead these items are considered as part of the environmental baseline.

However, some information regarding the structures and past operation and maintenance is included in this section to help describe the current and future operations of the Project.

maintenance actions included in the 2018 BA with Appendices A and B, plus Alternative 7 and Appendix A of the SEIS.

Figure 1. Diagram of the federally owned portion of the Project. Numbers in the diagram correspond to sections in

Chapter 1 of the 2018 BA, the shaded area is owned by the Corps. Mill Creek flows from right to left in the diagram (Corps 2018a).

Described generally, the O&M of the Project consists of three major elements. The first is the operation of the Mill Creek Diversion Dam (RM 11.4), the first Division Dam (RM 10.5), and associated canals, channels and structures to regulate flow for flood control, irrigation water delivery, and support of recreational facilities. Secondly, O&M of the Project includes vegetation management within the federally-managed portion of the Project, including vegetation that contributes to the function of habitat for ESA-listed fish. Finally, O&M of the Project includes structural and mechanical maintenance of the facilities within the federally-managed portion of the Project. A complete description of the numerous structures and their O&M follows below.

As mentioned previously, the structural components of the Project are divided into two sections based on ownership and management responsibility. From downstream to upstream: (1) RM 4.8 to 10.4 is locally owned and managed by the MCFCZD and; (2) RM 10.4 to approximately 11.5 is the federally-owned and managed portion. The locally owned and managed portion consists of approximately four miles of riprapped levees and channel spanning weirs, and two miles of concrete channel, some of which is underground. The federal portion consists of two dams, the Division Dam and the Mill Creek Diversion Dam, approximately 1.1 miles of stabilized channel between the 2 dams, 556 acres of nearby land and open water (Bennington Reservoir), and 2 canals to drain the reservoir (Russel Creek Outlet Channel and Mill Creek Return Canal). The purpose of the locally managed section is to convey as much water as possible as rapidly as possible through Walla Walla to reduce the risk of flooding, a function that is likely to be maintained regardless of how the federal portion of the Project is managed. We considered whether or not the proposed action would cause any other activities. After reviewing the Corps’ proposed action, NMFS determined that the O&M of the locally owned and managed portion occurs independently of the proposed action on the federally-owned portion and are thus not a consequence caused by the proposed action (50 CFR 402.02). Therefore, the O&M activities in the locally-managed portion of the Project are not analyzed as effects of the action.

The proposed action consists of all of the current and future O&M actions; construction of a new fish ladder at the first Division Dam completed and operational October 30, 2020; a new Diversion Dam fish ladder to be designed by the end of FY 2023 and constructed at Mill Creek Diversion Dam by the end of FY 2025; and design and construction of a low-flow channel by the end of FY 2030, subject to availability of funding (Corps 2018d). The proposed action also includes any O&M changes that arise from operation of the new fish ladders installed at the Division Dam and Mill Creek Diversion Dam. The proposed action includes the continued use of 1,700 cfs as the flow level at which unscreened diversions take place (in effect since March 2017) as described more fully below. The O&M of the Project also includes vegetation management within the federally-managed portion of the Project.

Operations generally consist of the opening and closing of various gates and the two fish ladders and vary based on the amount of flow entering the action area. There are three flow-based operating regimes; one for flows up to 400 cfs, another for flows between 400 cfs and 1,700 cfs, and another for flows exceeding 1,700 cfs. We do not attempt to describe or analyze emergency conditions. In the event of an emergency, the Corps would act as necessary to protect life and property according to the Corps’ mission, and conduct any required environmental reviews and consultations as soon as possible when the emergency is resolved.

The Corps operates the Project year round. While most maintenance activities will occur during the warmer months, some maintenance actions also occur year round (Corps 2018a ).

All planned in-water work activities would occur during the normal in-water work window of August 1 to September 30 unless coordinated with NMFS, USFWS, and the Washington Department of Fish and Wildlife (WDFW).

In December 2018, the Corps provided NMFS with the following timeline and reporting framework (Table 1) for three structural modifications the Corps proposes to implement beginning in FY 2020. Each of the three actions will contribute toward the goal of providing passage through the federal footprint at a much wider range of flows than is currently possible and improving habitat conditions during low-flow season (Corps 2018a; 2018d). After discussion with the Corps,5 NMFS assumes the low-flow channel components of the action will begin by FY 2025 if not sooner, and will take several years to complete (Corps 2018d).

5 Personal communication from B.Tice, Corps fisheries biologist September 5, 2019.

Table 1. Actions that the Corps will implement beginning in FY 2020 to remove passage barriers on the federal section of the Project (Corps 2018b).

Fiscal Year

(FY)

Division Works Ladder

Diversion Dam Ladder

Low-flow Channel

2019 Construction contract awarded

Complete 30 percent design and cost estimate on selected alternative*

Funding requested annually. Report to NMFS annually on funding status.

2020 Constructed and operational as of October 30, 2020.

Funding requested annually. Report to NMFS annually on funding status. Continued design and construction as funding becomes available.

2021 Operate and maintain annually.

Funding requested annually. Report to NMFS annually on funding status. Continued design and construction as funding becomes available

2022-

Complete design by the end of FY 2023* Request funding sufficient to construct by the end of FY 2025.

Funding requested annually. Report to NMFS annually on funding status. The timing and final design are not complete, although the Corps estimates completion of construction by end of FY 2030.

The following sections first discuss the operations of the numerous structural components under different flows (section 1.3.1), then Project maintenance and proposed structural changes (section 1.3.2).

1.3.1 Operations of the Structural Components of the Mill Creek Flood Control Project

Mill Creek Diversion Dam, Low-Flow Outlet, Fish Ladder

The Mill Creek Diversion Dam was constructed in 1942 with two low-flow outlets but no fish ladder for upstream fish passage until 1982. In 1982, one of the low-flow outlets was replaced with a fish ladder. The Mill Creek Diversion Dam is located on Mill Creek at RM 11.4 with the forebay and the federal boundary extending upstream approximately 1,000 additional feet to RM

11.5. Structures associated with the dam consist of the low-flow outlet, fish ladder, spillway, intake canal headworks, Mill Creek Diversion Dam dike, and debris barriers. The purpose of the Mill Creek Diversion Dam is to raise the water level behind the dam during floods to make it possible to divert floodwaters from Mill Creek through the intake canal headworks to the intake canal and into an off-channel reservoir, Bennington Reservoir. During normal operations (currently described as flows less than 1,700 cfs) the natural flow in Mill Creek passes either through the low-flow outlet and the fish ladder or over the Mill Creek Diversion Dam and downstream through the Project. When flows are less than 400 cfs, water passes through the dam via the low-flow outlet and fish ladder. For flows above 400 cfs, the outlet and ladder are closed and water passes over the spillway. Flows above 1,700 cfs are considered flood levels and the fish ladder and low-flow outlet remain closed while flows are divided between spilling over the dam and being diverted unscreened into Bennington Reservoir. This action is described in detail below.

Low-Flow Outlet

The low-flow outlet is located on the south side of the spillway adjacent to the fish ladder and passes water through the dam into the stabilized channel. The Corps controls the amount of flow passing through the outlet with an automatic gate. A small stilling basin is located downstream of the low-flow outlet channel and fish ladder. Fish heading upstream encounter the low-flow outlet before the fish ladder. A high velocity water jet from the low-flow outlet fans out until it impinges on the shoreline, creating a potential barrier for fish trying to find the ladder entrance.

Between the months of April and December, flows from the low-flow outlet are at least equal to fish ladder flows 60% of the time. In 2003 and 2004, the Corps used large concrete blocks to create a deeper entrance pool and direct some of the low-flow outlet jet away from the travel lane to the ladder entrance. This measure was considered ‘temporary’ but there are no plans to modify the low-flow outlet or the existing fish ladder. Upstream fish passage is assumed to be possible only through the fish ladder since the spillway is impassable and a combination of high water velocity and head pressure at the radial gate in the low-flow outlet likely forms a barrier.

Mill Creek Diversion Dam Fish Ladder

The Diversion Dam fish ladder was constructed in 1982 with a maximum design capacity flow of 42 cfs. Prior to that, any upstream fish movement had to be through the low-flow outlet. The ladder is located at the south end of the spillway, closest to the left bank with the low-flow outlet between the ladder and the spillway. The ladder is designed to operate fully open under normal conditions. Prior to 2004, the exit was operated partially closed to minimize debris (e.g., trees, limbs, and brush) problems. However, the Corps abandoned this method because of increased water velocity through the exit, which reduced fish passage. A grated walkway shades approximately 50 percent of the ladder. As mentioned above, a number of large concrete blocks were added on the north side of the ladder entrance in 2003 and 2004 as a temporary measure to concentrate the flow, help fish find the fish ladder entrance and create deeper water for improved passage.

When flows in Mill Creek are 42 cfs or less, approximately 20 cfs enters the ladder and the rest passes through the low-flow outlet. At flows greater than 42 cfs but less than 400 cfs, a greater proportion of water passes through the low-flow outlet compared to the fish ladder. While the fish ladder is designed to operate best at flows of 20 to 42 cfs, it remains open until flows reach 400 cfs with water divided between the low-flow outlet and the ladder. Video monitoring suggests that it begins to become a barrier at approximately 200 cfs (Corps 2018a). Water levels within the ladder vary from 0.5 to 2 feet at the entrance, 1.0 to 1.5 feet at the intermediate weirs, and 1 to 2 feet at the exit. The wide range of water levels at the entrance is caused by the varying amount of flow through the low-flow outlet and the water level in the stilling basin below the entrance. The water velocities inside the ladder are often too high, and the heights fish must jump are too high, complicating passage through the structure. The location of the low-flow outlet partially blocks the fish ladder entrance ‘attraction flow’, and the entrance becomes increasingly harder for upstream migrating salmonids to locate as flows increase (Corps 2018c). The ladder operates year round, except during maintenance or when flow is expected to exceed 400 cfs.

During periods of flows greater than 400 cfs, the ladder is manually closed. If flow is projected to reach or exceed 400 cfs for longer than 24 hours, the low-flow outlet is also closed, the forebay fills, and water flows over the spillway. As flow recedes, as much water as possible is passed through the fish ladder, and the remainder is passed through, or leaks around, the low-flow outlet gate. When the risk of needing to divert flows into the Reservoir for flood storage has passed, some screened water (diverted through fish screens) is also diverted to fill Bennington Reservoir to benefit fish and wildlife and recreation (See Figure 1).

When flows are over 400 cfs but less than 1,700 cfs (flood level, explained below) and the ladder and low-flow outlet are closed, all flow goes over the dam. When flows decline to near 400 cfs the Corps reduces the flow over the dam slowly, over a period of hours to allow any fish in the stilling basin time to move back into the channel. The Corps also inspects the stilling basin before it is completely dewatered using seines if necessary to “herd” any fish that are found toward the exit and back into the main channel before flows over the dam stop.6

Mill Creek Diversion Dam and Regulating Mill Creek Flows

During flood events, the Corps operates the Project to store excess floodwater in Bennington Reservoir that would otherwise cause flood damage to the City of Walla Walla. By reducing flood flows through the City of Walla Walla and downstream areas, the risk of property damage and loss of life caused by flooding is also reduced. The Corps operates the Project during such events according to the Water Control Manual (Manual) for the Mill Creek Project (Corps 2018b).

Under normal flow (below 400 cfs), the dam is operated to maintain enough water depth in the forebay to operate the fish ladder. As flow fluctuates, a sensor monitors the water level and adjusts the outlet gate automatically. As described above, when flow higher than 400 cfs is forecast to last more than 24 hours, the low-flow outlet and fish ladder gates are manually closed, the forebay fills, and all flow passes over the spillway (if conditions warrant, some of the flow is diverted to Bennington Reservoir). The spillway has a short downstream concrete stilling basin with concrete energy dissipaters, and it discharges into the Mill Creek stabilized channel.

When Mill Creek flow at the RM 10.4 stream gage reaches 1,000 cfs, the Corps initiates a decision process in accordance with the Manual to determine whether to divert water to Bennington Reservoir and how much to divert. Although the Corps initiates this decision process at 1,000 cfs, they do not divert unscreened floodwater into Bennington Reservoir until the flow in Mill Creek at the RM 10.4 stream gage is anticipated to reach 1,700 cfs (Corps 2018a). This 1,700 cfs flow is referred to as the ‘diversion trigger’ and has fluctuated over the years from 3,500 cfs to 1,100 cfs. Factors considered in this process include the following:

• Predicted amount of precipitation.

• Snowpack data.

• Forecasted temperature.

• Ground conditions (i.e., whether it is frozen).

6 Very limited reporting by the Corps indicates that adults are attracted into the stilling basin during high flows.

Most recent report April 22, 2019 observed three 24-inch steelhead in the basin when spill ended.

• Probability of another flood before the Reservoir can be drained.

• Increases or decreases in flow levels at upstream USGS Gages 14013000 and 14013700.

• Expected or reported damage to property, structures, infrastructure, etc.

• The amount of water currently in Bennington Reservoir (e.g., whether it is empty, half-full, etc.).

• River flow forecast from the National Weather Service River Forecast Center for the

Walla Walla River at Touchet, Washington RM 18.2 and near Kooskooskie, Washington on Mill Creek at RM 21.2.

The flow that remains in the Mill Creek channel downstream of the Mill Creek Diversion Dam after flood water is diverted into Bennington Reservoir is referred to as the regulated flow (natural flow – water diverted = regulated flow). Subsequent to the initial diversion trigger, the Water Control Manual directs increasing the amount diverted as the flood progresses and Bennington Reservoir fills. In other words, the diversion trigger is only the starting point for diversions. The amount diverted changes in response to actual conditions, increasing and decreasing with the natural flow with the intention to provide the maximum flood damage reduction possible.

The fish screens on the intake canal to Bennington Reservoir are designed to accommodate up to 30 cfs. When flows are expected to exceed 1,700 cfs, the screens are lifted up out of the canal and flows are diverted unscreened into the Reservoir until the flood event is over or until the reservoir elevation reaches established limits. The reservoir has no egress so fish that are diverted in the high flows are unable to return to Mill Creek. When the reservoir level exceeds the established limits, the regulated flow down the Mill Creek channel can be increased up to a maximum of 3,500 cfs as the flood flow increases.

Intake Canal and Intake Canal Headworks

The Corps diverts water into Bennington Reservoir through an intake canal. The intake canal headworks consists of four intake gates with a total design capacity of 7,000 cfs. The gates are controlled manually, but are powered by electric motors.

Diversions for Fish and Wildlife Propagation and Recreation

After the threat of flooding has passed, but prior to the end of the Corps’ water right on June 15, the Corps, on behalf of the WDFW, may divert up to 30 cfs (screened) from Mill Creek to fill Bennington Reservoir for public recreation, which includes fishing for trout and other fish stocked by WDFW. Under normal conditions, the Corps diverts up to 30 cfs until the Reservoir reaches an elevation of 1,205 feet. This typically takes 10 to 15 days to complete. Then the Corps diverts only enough water to maintain the Reservoir level at 1,205 feet until flow in the creek declines to 40 cfs. This is only necessary if winter and spring flows have not already filled the Reservoir.

Earthen Dike (Forebay Dike)

The north earthen dike forms the northern boundary of the Mill Creek Diversion Dam forebay and confines water to the main channel. The Corps uses goats or mowers to prevent any vegetation other than grass from becoming established.

Debris Barriers

Two debris barriers in the forebay help keep debris from damaging or blocking Project components. Debris is removed annually when the forebay is lowered.

Bennington Reservoir and Associated Storage Dam

Bennington Reservoir is an off-channel, man-made reservoir. While the reservoir has several ways of releasing water, it does not provide any mechanism for fish to escape; thus, fish diverted into the lake along with the unscreened high flows will remain in the reservoir.

The Reservoir intake tower is used to release water from the Reservoir into the Mill Creek Return Canal and the Russell Creek Outlet Channel (which flows into Yellowhawk Creek) to evacuate the reservoir or for maintenance. Each fall, the reservoir is drained via the Russell Creek Outlet Canal to enable inspection and maintenance of the intake tower. Draining the reservoir usually takes about 2 to 4 weeks. The amount of water released varies and depends on existing flows in Russell Creek. For maintenance purposes, the Corps does not release more than 20 cfs and flows are ramped up and down to prevent displacement in Russell or Yellowhawk Creeks, as outlined in the Corps Fish Passage Plan (FPP) (2007).

As described above, when Mill Creek flow exceeds 1,700 cfs, floodwaters are diverted to Bennington Reservoir to the maximum allowable level. Regardless of the flow at which waters are diverted, if the reservoir rises above elevation 1,212 feet, water is released from the reservoir through the intake tower to the either the Russell Creek Outlet Channel or the Mill Creek Return Canal.

Mill Creek Return Canal

The Mill Creek Return Canal is about 1-mile long and is designed to carry a flow of up to 190 cfs. Water discharges from the canal into Mill Creek just upstream of the Division Dam and Project office. The canal is used to return water to Mill Creek from the reservoir. Fish have no access to this canal nor is water released through it at a time or manner when it can be a measurable influence on Mill Creek flows.

Russell Creek Outlet Channel

The Russell Creek Outlet Channel is a 7,300-foot-long, concrete-lined, open channel, with a design discharge capacity of 250 cfs. The channel discharges into Russell Creek, a tributary of Yellowhawk Creek. The Corps uses the outlet channel immediately after flood diversions, often in conjunction with the Mill Creek Return Canal, to send up to 65 cfs to Russell Creek to maintain the Reservoir level below 1,212 feet elevation for dam safety.