Attch_8_-_Amend_0002_NMFS_Programmatic_0002.pdf

UNITED STATES DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

NATIONAL MARINE FISHERIES SERVICE

West Coast Region 1201 NE Lloyd Blvd., Suite 1100

PORTLAND, OREGON 97232-1274

Refer to NMFS No: WCR-2018-9898

March 11, 2019

Gregory Hughes, State Supervisor

U. S. Fish and Wildlife Service

1387 South Vinnell Way, Suite 368

Boise, Idaho 83709

Leanne Marten, Regional Forester

U.S. Forest Service Northern Region

P.O. Box 7669

Missoula, Montana 59807

Nora Rasure, Regional Forester

U.S. Forest Service Intermountain Region

324 25th Street

Ogden, Utah 84401

Curtis Elke, State Conservationist

Natural Resources Conservation Service

9173 West Barnes Drive, Suite C

Ferron Peterson, Program Manager

Bureau of Reclamation, Snake River Area

1150 North Curtis Road

Boise, Idaho 83706

Lt. Col. Christian N. Dietz

U.S. Army Corps of Engineers

Walla Walla District

201 N. Third Avenue

Walla Walla, WA 99362-1826

Tim Murphy

Idaho State Director

Bureau of Land Management

1387 South Vinnell Way

Re: Reinitiation of the Programmatic Endangered Species Act Section 7 Formal Consultation and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat

Consultation for Habitat Restoration Projects in the Salmon River Basin (HUC 170602), Clearwater River Basin (HUC 170603), Hells Canyon Subbasin (HUC 17060101), and

Lower Snake-Asotin Subbasin (HUC 17060103), Idaho

Dear Mr. Hughes, Ms. Marten, Ms. Rasure, Mr. Elke, Mr. Peterson, Lt. Col. Dietz, and Mr.

Murphy:

The enclosed document contains a reinitiated programmatic biological opinion (Opinion) prepared by the National Marine Fisheries Service (NMFS) pursuant to section 7(a)(2) of the

Endangered Species Act (ESA) (16 U.S.C. 1531 et seq.) on the effects of Habitat Restoration

Projects in Idaho. This Opinion, WCR-2018-9898, supersedes the previous Opinion issued for this same action, WCR-2014-832. Habitat Restoration Projects will be funded, permitted, or implemented by NOAA’s National Marine Fisheries Service (NMFS), the U.S. Army Corps of

Engineers (COE), the Bureau of Reclamation (BOR), the Natural Resources Conservation

Service (NRCS), the U.S. Forest Service (USFS), and the Bureau of Land Management (BLM).

Based on a review of monitoring data from habitat restoration projects implemented under this programmatic consultation between 2015 and 2017, NMFS determined that fish handling actions exceeded the extent of take for ESA-listed salmonids in our previous Opinion (WCR-2014-832), triggering reinitiation. NMFS therefore amended the biological assessment (BA) and prepared the attached revised Opinion (WCR-2018-9898). Procedures, activities included, and conservation measures for this programmatic ESA consultation remain largely the same. We encourage all of the action agencies to continue to use this programmatic consultation for efficient ESA consultation on routine aquatic habitat restoration projects.

In this Opinion, NMFS concludes that the action, as proposed, is not likely to jeopardize the continued existence of Snake River sockeye salmon, Snake River fall Chinook salmon, Snake

River spring/summer Chinook salmon, and Snake River Basin steelhead, or result in the destruction or adverse modification of designated critical habitat for these species.

As required by section 7 of the ESA, NMFS provides an incidental take statement (ITS) with the

Opinion. The ITS describes reasonable and prudent measures (RPMs) NMFS considers necessary or appropriate to minimize the impact of incidental take associated with this action.

The take statement sets forth nondiscretionary terms and conditions, including reporting requirements, that the federal agency and any person who performs the action must comply with to carry out the RPMs. Incidental take from actions that meet these terms and conditions will be exempt from the ESA take prohibition.

This document also includes the results of our analysis of the action’s likely effects on essential fish habitat (EFH) pursuant to section 305(b) of the Magnuson-Stevens Fishery Conservation and

Management Act (MSA), and includes three Conservation Recommendations to avoid, minimize, or otherwise offset potential adverse effects on EFH. These Conservation

Recommendations are a non-identical set of the ESA terms and conditions. Section 305(b)(4)(B) of the MSA requires Federal agencies to provide a detailed written response to NMFS within

30 days after receiving these recommendations.

If the response is inconsistent with the EFH Conservation Recommendations, the federal action agencies must explain why the recommendations will not be followed, including the justification for any disagreements over the effects of the action and the recommendations. In response to increased oversight of overall EFH program effectiveness by the Office of Management and

Budget, NMFS established a quarterly reporting requirement to determine how many

Conservation Recommendations are provided as part of each EFH consultation and how many are adopted by the action agency. Therefore, in your statutory reply to the EFH portion of this consultation, we ask that you clearly identify the number of Conservation Recommendations accepted.

If you have questions regarding this consultation, please contact Ms. Sarah Fesenmyer, Southern Snake Basin Branch Office, at (208) 378-5660, or sarah.fesenmyer@noaa.gov.

Sincerely, Michael P. Tehan Assistant Regional Administrator Interior Columbia Basin NOAA Fisheries, West Coast Region

Enclosure cc: S. Blihovde - USFWS T. Cracraft- NRCS E. Ellsworth - BLM B. Bohn-BLM D. Mitchell- COE W. Schrader - COE J. Trapani - BOR M. Edmondson - Idaho Governor's Office of Species Conservation D. Bertram- Idaho Governor's Office of Species Conservation S. Spaulding- USFS L. Jacobson - USFS H. Roerick - USFS C. Nalder - USFS B. Mitchell- USFS J. Lutes - USFS bcc: SBO: File copy; Read File; B. Lind; SBO Biologists

Molenaar:Lind:IDHabitatRestorProg:am:20190311:WCR-2018-9898 cc Addresses:

Stefanie Blihovde

U.S. Fish and Wildlife Service

Stefanie_blihovde@fws.gov

Trisha Cracroft

Natural Resource Conservation Service trisha.cracroft@id.usda.gov

Ethan Ellsworth

Bureau of Land Management eellsworth@blm.gov

Bryce Bohn

Bureau of Land Management bbohn@blm.gov

Duane Mitchell

Duane.E.Mitchell@usace.army.mil

William C. Schrader

William.C.Schrader@usace.army.mil

Jude Trapani

Bureau of Reclamation jtrapani@usbr.gov

Mike Edmondson

Idaho Governor’s Office of Species

Conservation

Mike.Edmondson@osc.idaho.gov

Scott Spaulding

U.S. Forest Service scottspaulding@fs.fed.us

Lee Jacobson

U.S. Forest Service ljacobson@fs.fed.us

Herbert Roerick

Boise National Forest hroerick@fs.fed.us

Clayton Nalder

Payette National Forest claytonnalder@fs.fed.us

Brenda Mitchell

Sawtooth National Forest brendalmitchell@fs.fed.us

Jim Lutes

Nez Perce Clearwater National Forest jamesrlutes@fs.fed.us

Daniel Bertram

Office of Species Conservation

Daniel.Bertram@osc.idaho.gov

Reinitiation of the Endangered Species Act Section 7(a)(2) Programmatic Biological Opinion and

Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Consultation

Habitat Restoration Projects in the Salmon River Basin (HUC 170602), Clearwater River Basin (HUC 170603), Hells Canyon Subbasin (HUC 17060101), and

Lower Snake-Asotin Subbasin (HUC 17060103), Idaho

NMFS Consultation Number: WCR-2018-9898

Action Agencies: National Marine Fisheries Service, U.S. Army Corps of Engineers, Bureau of Reclamation, Natural Resources Conservation Service, U.S .- Forest Service, and the Bureau of Land Management

Aftec e tdS,pec1es an dDte ermma 10ns:

ESA-Listed Species Status

Is Action Likely to Adversely Affect Species or Critical

Habitat?

Is Action Likely to Jeopardize the

Species?

Is Action Likely to Destroy or

Adversely Modify Critical Habitat?

Snake Ri ver Bas in steelhead (Oncorhynchus mykiss)

Threatened Yes No No

Snake River fall Chinook (0 . tshawytscha)

Threatened Yes No No

Snake River spring/summer Chinook

(0. tshawytscha)

Threatened Yes No No

Snake Ri ver sockeye salmon (0. nerka)

Endangered )'es No No

Fishery Management Plan that Describes EFH in the Project Area

Does Action Have an Adverse Effect on EFH?

Are EFH Conservation Recommendations Provided?

Pacific Coast Salmon Yes Yes

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

~~t)gk-Issued By:

Michael P. Tehan Assistant Regional Administrator

Date: March 11, 2019 i

TABLE OF CONTENTS

1. INTRODUCTION

1.1 Background

1.2 Consultation History

1.3 Proposed Action

1.3.1 Action Agencies

1.3.2 Program Implementation Procedures

1.3.3 Categories of Habitat Restoration Activities

1.3.4 General Conservation Measures

1.3.4.1 Pre-construction and Project Design Conservation Measures

1.3.4.2 Construction Conservation Measures

1.3.4.3 Post-construction Conservation Measures

1.3.5 Action Categories and Specific Conservation Measures

1.3.5.1 Fish Screening

1.3.5.2 Fish Passage

1.3.5.3 Construction or Improvement of Fish Passage Structures

1.3.5.4 Removal or Modification of Water Control Structures (e.g., Diversion Structures) 20

1.3.5.5 Bridge and Culvert Replacement or Removal

1.3.5.6 Instream Flow

1.3.5.7 Instream Structures

1.3.5.8 Channel Reconstruction/Relocation

1.3.5.9 Riparian Habitat

1.3.5.10 Removal of Non-native Invasive Plants

1.3.5.11 Streambank Stabilization

1.3.5.12 Road and Trail Erosion Control, Maintenance and Decommissioning

1.3.5.13 Surveying and Monitoring

2. ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL TAKE

STATEMENT

2.1 Analytical Approach

2.2 Rangewide Status of the Species and Critical Habitat

2.2.1 Status of Listed Species

2.2.1.1 Snake River Spring/Summer Chinook Salmon

2.2.1.2 Snake River Basin Steelhead

2.2.1.3 Snake River Fall Chinook Salmon

2.2.1.4 Snake River Sockeye Salmon

2.2.2 Status of Critical Habitat

2.2.3 Climate Change Implications for ESA-listed Species and their Critical Habitat

2.3 Action Area

2.4 Environmental Baseline

2.4.1 Biological Requirements of Salmonids

2.4.2 Effects of Land Management and Development

2.4.3 Basins in Action Area

2.5 Effects of the Action

2.5.1 Long-term Benefits to Salmonids and their Habitat

2.5.2 Short-term Adverse Effects to Salmonids and their Habitat ii

2.5.2.1 Noise and Disturbance

2.5.2.2 Fish Handling

2.5.2.3 Suspended Sediment

2.5.2.4 Sediment Deposition

2.5.2.5 Temperature

2.5.2.6 Chemical Contamination

2.5.2.7 Herbicides

2.5.3 Effects to Designated Critical Habitat

2.5.3.1 Water Quality

2.5.3.2 Substrate/Spawning Gravel

2.5.3.3 Forage

2.5.3.4 Riparian Vegetation

2.6 Cumulative Effects

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. MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT

ESSENTIAL FISH HABITAT CONSULTATION

3.1 Essential Fish Habitat Affected by the Project

3.2 Adverse Effects on Essential Fish Habitat

3.3 Essential Fish Habitat Conservation Recommendations

3.4 Statutory Response Requirement

3.5 Supplemental Consultation

4. DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW . 112

4.1 Utility

4.2 Integrity

4.3 Objectivity

5. REFERENCES

APPENDIX A ............................................................................................................................. A-1

APPENDIX B ............................................................................................................................. B-1

APPENDIX C ............................................................................................................................. C-1

APPENDIX D ............................................................................................................................. D-1

TABLES

Table 1. Subbasins in Idaho with ESA-listed anadromous fish Table 2. Categories of activities under the proposed action Table 3. Active ingredients and end-use products that may be used for weed control

Table 4. Buffer restrictions associated with herbicide use iii

Table 5. Additional buffer restrictions for different herbicide application methods and different windspeeds Table 6. Listing status, status of critical habitat designations and protective regulations, and relevant Federal Register decision notices for ESA-listed species considered in this

Opinion Table 7. Summary of viable salmonid population parameter risks and overall current status for each population in the Snake River spring/summer Chinook salmon ESU

(NWFSC 2015)

Table 8. Summary of viable salmonid population parameter risks and overall current status for each population in the Snake River Basin steelhead distinct population segment

(NWFSC 2015). Risk ratings with “?” are based on limited or provisional data series Table 9. Types of sites, essential physical and biological features, and the species life stage each PBF supports Table 10. Geographical extent of designated critical habitat in Idaho for ESA-listed anadromous species Table 11. Potential short-term adverse effects from each category of action

Table 12. Estimates for the number of salmon and steelhead juveniles that will be disturbed, injured, or killed from netting, electrofishing, and dewatering annually

Table 13. Physical properties, application rates, and estimated environmental concentrations for herbicides proposed for use Table 14. Toxicity of active ingredients and adjuvants proposed for use under this program. . 98

Table 15. Comparison of estimated environmental concentrations of herbicide active ingredients to known toxicities to salmonids and their prey species Table 16. Toxicity values for surfactants proposed for use under this program

FIGURE

Figure 1. Subbasins in Idaho occupied by ESA-listed anadromous fish species

ACRONYMS

Acronym Definition

1µPa microPascal

BA Biological Assessment

BDA Beaver Dam Analog

BLM Bureau of Land Management

BOR Bureau of Reclamation

BPA Bonneville Power Administration

COE U.S Army Corps of Engineers

CWA Clean Water Act dB Decibel

DPS Distinct Population Segment

DQA Data Quality Act

EEC Estimated Environmental Concentration iv

Acronym Definition

EFH Essential Fish Habitat

ELJ Engineered Logjam

EPA U.S. Environmental Protection Agency

ESA Endangered Species Act

ESU Evolutionarily Significant Unit

FCRPS Federal Columbia River Power System

HUC Hydrologic Unit Code

ICBTRT Interior Columbia Basin Technical Recovery Team

IDEQ Idaho Department of Environmental Quality

IDFG Idaho Department of Fish and Game

ITS Incidental Take Statement

LWD Large Woody Debris mg/L milligrams per Liter

MPG Major Population Group mph miles per hour

MSA Magnuson–Stevens Fishery Conservation and Management Act

MSO Methylated Seed Oil

NMFS National Marine Fisheries Service

NRCS Natural Resources Conservation Service

NTU Nephelometric Turbidity Units

OHWM Ordinary High Water Mark

Opinion Biological Opinion

PALS Post-Assisted Log Structures

PBF Physical and Biological Features

PCE Primary constituent element

PCSRF Pacific Coast Salmon Recovery Fund

PIT Passive Integrated Transponder

PLWW Post Lines with Wicker Weaves

RPM Reasonable and Prudent Measure

SAR Smolt-to-Adult Return

Screen Shop Idaho Department of Fish and Game Screen Shop

SERA Syracuse Environmental Research Associates, Inc.

SWS Small Woody Structures

USFS United States Forest Service

USFWS U.S. Fish and Wildlife Service

VSP Viable Salmonid Populations

WAF Water Accommodated Fraction

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 biological opinion (Opinion) and incidental take statement (ITS) portions of this document in accordance with section 7(b) of the

Endangered Species Act (ESA) of 1973, as amended (16 U.S.C. 1531, et seq.), and implementing regulations at 50 CFR 402. We also completed an essential fish habitat (EFH) consultation on the proposed action, 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 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

(DQA) (section 515 of the Treasury and General Government Appropriations Act of 2001, Public Law 106-5444). A complete record of this consultation in on file at the Snake River

Basin Office, Boise, Idaho.

1.2 Consultation History

NMFS, U.S. Army Corps of Engineers (COE), Bureau of Reclamation (BOR), Natural

Resources Conservation Service (NRCS), U.S. Forest Service (USFS), and the Bureau of Land

Management (BLM), collectively called the action agencies, initiated a programmatic consultation for routine aquatic habitat restoration projects throughout 18 subbasins in central

Idaho (Table 1). Although NMFS is the lead action agency for this consultation, all of these action agencies fund, permit, or implement stream restoration projects in central Idaho. Such projects will restore degraded habitat conditions and promote recovery of ESA-listed salmon and steelhead. NMFS estimates that the action agencies will collectively implement between 10 and

20 projects per year under this programmatic consultation, based on the number of individual consultations in past years on habitat restoration projects. However, NMFS recognizes that this is not an upper limit, and a greater number of projects per year are possible. Projects are likely to occur throughout central Idaho.

Table 1. Subbasins in Idaho with ESA-listed anadromous fish.

4th-field Hydrologic Unit Code (HUC) HUC Name

17060101 Hells Canyon

17060103 Lower Snake-Asotin

17060201 Upper Salmon

17060202 Pahsimeroi

17060203 Middle Salmon-Panther

17060204 Lemhi

17060205 Upper Middle Fork Salmon

17060206 Lower Middle Fork Salmon

4th-field Hydrologic Unit Code (HUC) HUC Name

17060207 Middle Salmon-Chamberlain

17060208 South Fork Salmon

17060209 Lower Salmon

17060210 Little Salmon

17060301 Upper Selway

17060302 Lower Selway

17060303 Lochsa

17060304 Middle Fork Clearwater

17060305 South Fork Clearwater

17060306 Clearwater

NMFS drafted a biological assessment (BA) and circulated the first draft to the other action agencies on July 9, 2013. NMFS then revised the BA in response to suggestions from the other action agencies on how to refine the description of the action and provide appropriate conservation measures and protocols. On October 21, 2013, NMFS circulated a revised BA to the action agencies. On December 6, 2013, NMFS met with the U. S. Fish and Wildlife Service

(USFWS) to discuss the proposed action. Between December 2013 and March 2014, NMFS worked with the USFWS to further refine the proposed action in order to minimize impacts to bull trout (Salvelinus confluentus) and terrestrial ESA-listed species. NMFS finalized the BA and submitted it to USFWS on May 28, 2014. NMFS’ 2014 Opinion (WCR-2014-832) on this action was based on information provided in that BA.

2019 Revised Biological Opinion. Based on review of 39 monitoring reports from restoration activities taking place from 2015 through 2017, NMFS determined that the amount of incidental take described in our 2014 Opinion had been exceeded through fish salvage activities, thereby requiring this reinitiation of consultation. Monitoring results from the projects implemented in

2015 through 2017 provided a more accurate estimate of the number of fish that might be handled during salvage activities, accounting for the size of each project and the potential fish densities within each project action area. Based on this information, NMFS revised the BA and prepared this Opinion. The amended BA includes an expansion of the proposed action to include one additional action category, and the modification and clarification of two existing habitat action categories. Specifically, small woody structures (SWS) (e.g., beaver dam analogs

[BDAs], wicker/willow weaves, etc.) will be added to the Instream Structures category, and the

Fish Passage, and the Road and Trail Erosion Control, Maintenance, and Decommissioning categories have been revised. In addition, the General Conservation Measures have been revised to minimize effects to ESA-listed salmonids and increase efficiency in implementation of conservations measures.

Because this action has the potential to affect tribal trust resources, we provided copies of the draft Opinion to the Nez Perce Tribe and Shoshone-Bannock Tribes on February 4, 2019. The

Nez Perce Tribe responded that they did not have comments. We did not receive comments from the Shoshone-Bannock Tribes.

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 the larger action for their justification. Interdependent actions are those that have no independent utility apart from the action under consideration (50 CFR

402.02). There are no interrelated or interdependent actions associated with this action. The proposed action is the funding, permitting, or implementation of routine aquatic habitat restoration projects by one or more of the action agencies.

1.3.1 Action Agencies

The action agencies in this programmatic consultation are NMFS, COE, BOR, NRCS, USFS, and the BLM. Here we describe the mechanisms through which each agency funds, permits, or implements habitat restoration projects in Idaho.

NMFS provides funding for habitat restoration projects through the Pacific Coast Salmon

Recovery Fund (PCSRF) and the Mitchell Act. The PCSRF was established by Congress to protect, restore, and conserve Pacific salmon and steelhead populations and their habitats. Under the PCSRF, NMFS manages a program to provide funding to states (including Idaho) and tribes of the Pacific Coast region. Congress passed the Mitchell Act in 1938 to provide for the conservation of salmon and steelhead fishery resources of the Columbia River. One component of the program is the construction, operation, and maintenance of screens at irrigation diversions to protect juvenile salmon and steelhead in Oregon, Washington, and Idaho. This component has been addressed in an existing informal consultation. This consultation incorporates by reference the analysis contained in the existing informal consultation on the Mitchell Act Irrigation

Diversions Screening Programs, completed on January 31, 2000 (NWR-2014-697). The informal consultation covered the construction, operation, and maintenance of fish screens under the Mitchell Act program, except for projects involving significant instream construction. This programmatic habitat restoration consultation will also cover inwater work activities associated with fish screen installations that were not covered in the January 31, 2000, Mitchell Act informal consultation.

The COE regulates activities in waters of the United States through section 404 of the Clean

Water Act (CWA) of 1972 and Section 10 of the Rivers and Harbors Act of 1899. Under

Section 404 of the CWA, a Department of the Army permit, issued through the COE, is required for the discharge of dredged or fill material into all waters of the United States, including special aquatic sites such as wetlands and vegetated shallows. Under Section 10 of the Rivers and

Harbors Act, a Department of the Army permit, issued through the COE, is required for any structure or work that occurs in, above or under navigable waters of the United States or affects the course, location, condition or capacity of such waters. Habitat restoration projects that alter stream channels or streambanks often require a permit from the COE.

The BOR works in partnership with local landowners, representatives from states, tribes, other

Federal agencies, and conservation groups on habitat projects to improve spawning and rearing habitat for Columbia River basin salmon and steelhead listed under the ESA. The BOR’s

Tributary Habitat Program was initiated in 2000 to mitigate for the impacts of the Federal

Columbia River Power System (FCRPS) on salmonids. The program is focused on providing technical services including project coordination, environmental compliance, permit application, engineering design, and construction monitoring to local project sponsors who obtain Federal, state, and private funding to construct the habitat projects. In Idaho, BOR’s Tributary Habitat

Program currently includes the Little Salmon, Upper Salmon, Lemhi, Yankee Fork, and

Pahsimeroi River subbasins, but could expand to other Idaho subbasins in the future. Projects in other subbasins occupied by ESA-listed anadromous fish will also be covered under this programmatic consultation. The BOR contributions focus on instream habitat projects that: (1)

Increase streamflow through acquisition or lease of water rights, or through improved irrigation efficiency; (2) remove barriers to improve access to a greater range of spawning and rearing habitat; (3) replace screens on water diversions to reduce entrainment of fish in water delivery systems; (4) increase channel complexity; or (5) reconnect side-channels and floodplains to main stream channels. The BOR currently focuses on the project categories listed above, but could engage in any of the other project categories included in this programmatic consultation.

The NRCS provides technical and financial assistance to private landowners and others for habitat restoration projects with funding the agency administers under the Federal Farm Bill.

The NRCS also participates as a partner organization in habitat restoration projects that utilize other funding sources. The NRCS contributes technical expertise in an array of disciplines to these projects.

The USFS administers public lands throughout Idaho, covering many miles of stream and riparian habitat. This consultation will cover USFS habitat restoration actions for which there is not a pre-existing consultation in place. For categories of habitat restoration activities for which the USFS has an existing programmatic consultation in place with NMFS for anadromous watersheds in Idaho (e.g., stream road crossings, weeds treatment), such activities will continue to be covered under the existing programmatic consultation, as explained below under descriptions of specific activity categories.

The BLM administers public lands throughout Idaho, covering many miles of stream and riparian habitat. This consultation will cover BLM habitat restoration actions for which there is not a pre-existing consultation in place. For categories of habitat restoration activities for which the BLM has an existing programmatic consultation in place with NMFS for anadromous watersheds in Idaho (e.g., stream road crossings, weeds treatment), such activities will continue to be covered under the existing programmatic consultation, as explained below under descriptions of specific activity categories.

1.3.2 Program Implementation Procedures

A habitat restoration project conducted under this consultation may involve multiple parties: one or more federal agencies, a Project Sponsor, a private landowner, and contractors. This Opinion refers to the Project Sponsor as the entity planning and implementing an individual project. The

Project Sponsor will most often be non-federal (e.g., Trout Unlimited or the Nez Perce Tribe), but could in some cases be the federal action agency itself (e.g., USFS). If there are multiple action agencies involved in an individual project, the action agencies will choose one agency to be the lead action agency for the project. The lead action agency will ensure that the Project

Sponsor follows all applicable conservation measures and submits all applicable pre- and post-project reports to NMFS and USFWS. A federal action agency may also choose to complete project documentation for the Project Sponsor (e.g., NRCS or COE working with a private landowner).

If one or more action agency intends to fund, permit, or carry out an individual project under this programmatic consultation, the lead action agency will first briefly confirm, via a phone call or email to the local NMFS biologist or NMFS Snake Basin Office in Boise, that the project will fit under the parameters and conservation measures of this programmatic. The lead action agency will then provide the Project Sponsor with a Project Information Form (Appendix A). The

Project Information Form will specify the lead action agency for the project. The lead action agency will ensure that the Project Sponsor completes and submits the Project Information Form to NMFS and USFWS (and simultaneously to all other action agencies involved in the project) at least 60 days before initiating the project (or 90 days in some cases, as explained below). NMFS and USFWS will review the project information and determine whether additional information or a site visit is necessary. If NMFS or USFWS determines that, a site visit is necessary, the Project

Sponsor and lead action agency will coordinate a site visit for NMFS and/or USFWS staff at least 30 days prior to the planned project start date. NMFS and USFWS will verify, through reviewing the Project Information Form and any additional information provided by the Project

Sponsor, or a site visit, that the project falls under this programmatic consultation. Before the project begins, a NMFS biologist will email the Project Sponsor (and all action agencies involved in the project) to confirm that the project fits under this programmatic consultation for listed anadromous species; and a USFWS biologist will email the Project Sponsor (and all action agencies involved in the project) to confirm that the project fits under this programmatic consultation for all other ESA-listed species. For complex projects with engineering plans, the

Project Sponsor will contact NMFS as early as possible in the project development phase to allow sufficient time for a NMFS and/or USFWS site visit and discussion of applicable project design and conservation measures.

If, during implementation of a restoration project, NMFS, USFWS, or the Project Sponsor becomes aware of new information or unforeseen circumstances such that the project cannot be completed according to the scope of effects or terms and conditions of the Opinion, then NMFS and USFWS will require that the Project Sponsor stop all project operations, except for efforts to avoid or minimize resource damage, pending completion of individual consultation on the project.

The Project Sponsor will email the Project Information Form to NMFS

(nmfswcr.srbo@noaa.gov), USFWS (Stefanie_blihovde@fws.gov), and to all other action agencies included in the project. The Project Sponsor will submit the Project Completion Form

(Appendix B) to NMFS and USFWS within 90 days of project completion, to the same email addresses as above. If the project required dewatering for instream work, the Project Completion

Form will describe all fish handling. The Project Sponsor will also list on the form any herbicides used. Reasonable land access for post-project monitoring will be a condition required for any permits covered under this programmatic.

For some restoration categories, the Project Sponsor will submit engineering plans to NMFS

(attached to the Project Notification Form) so that NMFS can evaluate the plans for their consistency with NMFS’ fish passage criteria. All projects will follow NMFS’ most recent passage criteria1; the current criteria at this time is NMFS’ Anadromous Salmonid Passage

Facility Design (NMFS 2011a). NMFS will review engineering plans for installing or modifying fish passage structures to ensure consistency with these criteria. The Project Sponsor will submit engineering plans at least 90 days before the planned project start date. The Project Sponsor will email the engineering plans to NMFS along with the Project Notification Form to nmfswcr.srbo@noaa.gov. The categories requiring engineering review include fish screens, fish passage facilities at dams, new diversion structures, installation of grade control structures greater than 3-foot height aggregate, and channel reconstruction projects. A checklist of information to provide to NMFS is included in this BA for screens (Appendix C). For the other types of projects, the Project Sponsor will submit design plans and engineering calculations. The

Project Sponsor may need to adjust the project plans in response to NMFS review.

Each action agency in this consultation will submit an annual report to NMFS and USFWS by

April 1 each year, listing all projects completed under the programmatic consultation for the previous year. If NMFS deems it necessary, a representative from each action agency will participate in an annual meeting or phone call to discuss the implementation of the program, types of variances approved, how to improve conservation under the program, and how to make the program more efficient.

1.3.3 Categories of Habitat Restoration Activities

The proposed action consists of nine categories of restoration activities: (1) Fish Screening; (2)

Fish Passage; (3) Instream Flow; (4) Instream Structures; (5) Side Channels and Floodplain

Function; (6) Channel Reconstruction; (7) Riparian Habitat; (8) Road and Trail Erosion Control, Maintenance, and Decommissioning; and (9) Surveying and Monitoring. Table 2 lists these action categories and identifies specific action types included under each category. Some restoration projects may involve multiple categories.

NMFS estimates that the action agencies will collectively implement between 10 and 20 projects per year under this programmatic consultation, based on the number of individual consultations in past years on habitat restoration projects; however, a greater number of projects per year are allowed. Based on individual consultations in past years, projects under this programmatic consultation are likely to be distributed throughout action area (Figure 1); and the most frequent action categories are likely to be riparian restoration, channel and floodplain reconstruction, and instream flow projects.

Table 2. Categories of activities under the proposed action.

Action Category Specific Actions Included in the Consultation

Fish Screening Install, upgrade, or maintain fish screens (NMFS must review engineering plans for installation or upgrading of screens).

1 At the time of publishing this Programmatic, NMFS was in the process of updating its fish passage design criteria but NMFS

(2011a) contained the current criteria. Inquire with NMFS to ensure the applicant has NMFS’ current criteria document.

Fish Passage

Install or improve fish passage facilities (e.g., fish ladders or other fishways) at diversion structures and other passage barriers (NMFS must review engineering plans).

Remove or modify water control structures (e.g., irrigation diversion structures).

Replace culverts and bridges to provide fish passage and/or to reduce risk of culvert failure and chronic sedimentation, using the stream simulation methods from NMFS (2011b).

Instream Flow

Lease or purchase water rights to improve instream flows.

Change or consolidate points of diversion (NMFS must review engineering plans).

Increase efficiency of irrigation practices (e.g., convert open ditches to pipes, or convert surface water diversions to ground water wells).

Instream Structures

Provide grade control with boulder weirs or roughened channels (NMFS must review engineering plans for installation of structures greater than 3 feet high).

Install instream habitat structures including:

Root wads, large woody debris (LWD), and log jams;

Boulders;

Spawning gravels; and, Small Woody Structures.

Side Channels and

Floodplain Function

Reconnect and restore historic side channels.

Modify or remove levees, dikes, berms, and fill.

Channel Reconstruction Reconstruction of existing stream channels into historic or newly constructed channels (NMFS must review engineering plans).

Riparian Habitat

Plant riparian vegetation.

Reduce riparian impacts from livestock:

Install fencing;

Develop livestock watering facilities away from streams; and, Install livestock stream crossings (culverts, bridges, or hardened fords).

Control invasive weeds through physical removal or with herbicides.

Stabilize streambanks through bioengineering.

Road and Trail Erosion

Control, Maintenance, and Decommissioning

Decommission or obliterate unneeded roads.

Relocate portions of roads and trails away from riparian buffer areas.

When part of a larger restoration project, reduce sediment from existing roads, including:

Improve and maintain road drainage features.

Reduce road access and usage through gates, fences, boulders, logs, tank traps, and signs.

Remove or stabilize pre-existing cut and fill or slide material.

Surveying and

Monitoring

Survey project sites:

Take physical measurements;

Install recording devices; and, Determine fish presence (electroshocking for research purposes is not included under this consultation).

Monitor project site and stream habitat after project completion.

Install passive integrated transponder (PIT) tag detection arrays.

The activities covered under this consultation will be aimed at protecting or restoring fish and wildlife habitat, with long-term benefits for ESA-listed species. However, project construction activities may adversely affect ESA-listed species in the short term. In order to minimize these adverse effects, the proposed action includes a general set of conservation measures applicable to all projects, as well a set of conservation measures specific to each category of activity. This

Opinion first lists the general conservation measures, and then provides a detailed description of each action category, along with specific conservation measures for each category.

Figure 1. Subbasins in Idaho occupied by ESA-listed anadromous fish species.

1.3.4 General Conservation Measures

In order to minimize the magnitude and duration of short-term adverse effects on ESA-listed species and critical habitat, and to avoid a chance of long-term adverse effects, all projects under this programmatic consultation will comply with the following set of conservation measures.

1.3.4.1 Pre-construction and Project Design Conservation Measures

Timing of in-water Work. In-water work will occur only within the preferred work windows listed in Appendix D. For the Upper Salmon River Basin, the work windows are from Upper

Salmon Basin Watershed Project Technical Team (2005). If the Upper Salmon Basin Watershed

Technical Team updates this list, project sponsors will follow the most recent recommendations.

Fish Screens. All water intakes in which fish could be entrained and injured, including pumps used to isolate an in-water work area, will have a fish screen installed, operated, and maintained according to the criteria in NMFS (2011b or most current version).

Site Assessment for Contaminants. If an action involves excavation of more than 20 cubic yards of material in an area with past mining impacts or other land uses known to cause chemical contamination, then the Project Sponsor will complete a site assessment for contaminants.

Excavation could be for side-channel habitat restoration, or set-back or removal of an existing berm, dike or levee. The site assessment will include the following elements to identify the type, quantity, and extent of any potential contamination: (1) A review of readily available records, such as former site use, building plans, or records of any prior contamination events; (2) a site visit to observe the areas used for various industrial processes and the condition of the property;

(3) interviews with knowledgeable people, such as site owners, operators, occupants, neighbors, and local government officials; and (4) a report that includes an assessment of the likelihood that contaminants are present at the excavation site. If the site assessment finds potential for chemical contamination of surface waters from the action, then the project will not fit under the proposed action and individual consultation on the project will be necessary.

Site Layout and Flagging. Prior to construction, the action area will be flagged to identify the following: (1) Sensitive resource areas, such as areas below the ordinary high water mark

(OHWM), spawning areas, springs, and wetlands; (2) equipment entry and exit points; (3) road and stream crossing alignments; (4) staging, storage, and stockpile areas; and (5) no-spray areas and buffers for herbicides.

Temporary Erosion Controls. Temporary erosion controls shall be in place before any significant disturbance of soils, or loss of ground cover, and will be installed downslope of project activity within the riparian buffer area until site rehabilitation is complete. Once the site is stabilized, temporary erosion control measures must be removed.

Emergency Erosion and Chemical Spill Controls. The Project Sponsor will ensure that the following materials for emergency control of erosion and chemical spill control are onsite: (1)

An adequate supply of sediment control materials (e.g., silt fence, straw bales2); and (2) an oil-absorbing floating boom and absorbent pads whenever surface water is present.

Temporary Access Roads. The Project Sponsor will ensure the following conservation measures are applied to temporary access roads:

1. Do not build temporary access roads where grade, soil, or geomorphic features suggest slope instability, including slopes greater than 30 percent.

2. Minimize the removal of riparian vegetation when creating temporary access roads. The

Project Sponsor will estimate the amount of vegetation to be removed in the Project

Information Form.

2 Certified weed-free straw or hay bales will be used to prevent introduction of noxious weeds.

3. Minimize the number and length of temporary access roads, and design roads to avoid erosion and soil compaction.

a. Minimize soil disturbance and compaction whenever a new temporary road is located.

This may include easily disturbed wet areas or sensitive soils within 150 feet of a stream, waterbody, or wetland, by: clearing vegetation to ground level and placing clean gravel over geotextile fabric; or providing and documenting alternative erosion control measures that suit site conditions, unless otherwise approved in writing

(email) by NMFS.

4. At temporary stream crossings, equipment will cross the stream in the wet only under the following conditions:

a. No stream crossings may occur at sites where: (1) Adults are actively spawning, or immediately upstream (300 feet) of actively spawning adults; (2) holding adult ESA-listed fish are present; or (3) eggs or alevins are in the gravel.

b. Do not place temporary crossings in areas that may increase the risk of channel re-routing or avulsion, or in potential spawning habitat (e.g., pools and pool tailouts).

c. If temporary stream crossings are anticipated to exceed two round trips, use existing stream crossings, or install temporary bridges and culverts to allow for equipment and vehicle crossing to minimize impacts to ESA-listed fish species and habitat, unless otherwise approved by a NMFS and USFWS biologist.

d. Equipment and vehicles may cross the stream in the wet only where the streambed is bedrock and where the streambed is naturally stable, at existing hardened fords, or where mats or off-site logs are placed in the stream and used as a crossing. Vehicles and machinery will cross streams at right angles to the main channel wherever possible.

e. Where necessary to minimize impacts to the stream, and temporary stream crossings are anticipated to exceed two round trips, install temporary bridges and culverts to allow for equipment and vehicle crossing over wetted streams to access construction areas.

5. When the project is completed, all temporary access roads will be obliterated, and the soil will be stabilized and revegetated. Road obliteration refers to the most comprehensive degree of road decommissioning and involves decompacting the road surface and ditch, pulling the fill material onto the running surface, and reshaping the roadbed to match the hillside contour. The Project Sponsor will obliterate temporary roads in wet areas or areas prone to flooding as soon as possible after project completion and before the start of fall rains.

Choice and Use of Equipment. Heavy equipment will be selected (when possible) and operated in a manner that minimizes adverse effects to the environment (e.g., minimally-sized, low pressure tires, minimal hard turn paths for tracked vehicles, temporary mats or plates within wet areas or sensitive soils).

Vehicle Staging. All equipment shall be cleaned and leaks repaired at least 150 feet from any natural waterbody or wetland prior to entering the project area. The Project Sponsor will remove external oil and grease prior to arriving onsite. Thereafter, equipment will be inspected daily for leaks or accumulations of grease, and any identified problems fixed before operation within

150 feet of any natural waterbody or wetland.

Invasive Species. Inspect and, if necessary, wash vehicles and equipment to prevent introducing terrestrial invasive species prior to bringing equipment on the work site. Inspect and sanitize water craft, waders, boots, and any other gear to be used in or near water to prevent the spread of invasive species or whirling disease.

Erosion and Sediment Control. Erosion and sediment control are paramount considerations for all ground-disturbing construction activities, particularly when activities occur in or near waterways. The Project Sponsor will describe all temporary and permanent erosion and sediment control measures to be used during the project on the Project Information Form.

Erosion control measures will be appropriate for site and weather conditions. The following conservation measures are designed to prevent and minimize soil erosion, and to collect, retain, and treat stormwater runoff and pollutant discharges during all phases of construction:

1. A supply of emergency erosion control materials will be on hand; and temporary erosion controls will be installed and maintained in place until site restoration is complete unless site conditions, soils, etc., prevent effective use of temporary erosion controls. If the later of these options determines that no, or limited use of, emergency and temporary erosion controls is practicable, then the project practitioner will document the type of site conditions and why they limit or preclude use of erosion control measures. If site conditions exhibit exposed soils after completion of work, then temporary erosion control materials, composed of all-biodegradable material may be used.

2. Ground disturbance will not occur during wet conditions (i.e., during or immediately following rain events), depending on local soil conditions. If soil conditions do not require restricted ground disturbance, the project sponsor and practitioner will provide a geotech report, profiling soil types and erosion potential, to exclude project from this conservation measure.

3. Sequence or schedule work to reduce exposed bare soil subject to wind erosion. Water may be used to control dust, provided the water intake diversion does not pose dewatering risk to instream flows within the reach (see Conservation Measures in Section

1.3.5.6) and any intake pumps are properly screened to avoid entrainment and injury risk to fish (see Section 1.3.4).

4. Vegetation may be grubbed only from areas where permanent ground alteration will occur. Vegetation is to be cut at ground level and root wads retained where temporary clearing occurs.

5. Wood fiber mulch and tackifier (hydro-applied) may be used to reduce erosion of bare soil if the Project Sponsor provides certification from the manufacturer that the materials are noxious weed free and nontoxic to aquatic and terrestrial animals, soil microorganisms, and vegetation. This certification will be available for inspection upon request by NMFS and USFWS. See the Idaho Sate Noxious Weed List found in Idaho

Administrative Procedures Act 02.06.22 for a list of 64 different species of weeds which are designated noxious by state law.

6. Permanent soil stabilization outside the OHWM is best accomplished with reestablishment of native vegetation where possible. The Project Sponsor will begin site restoration immediately following completion of ground disturbing activities. Temporary soil stabilization measures (e.g., jute matting) are required until permanent measures are established and functioning properly. Guidance on selecting and planting native seed or plant materials, including plant densities and species composition, will be provided by technical experts familiar with local site conditions. See the following reports for detailed information on planting appropriate riparian vegetation: How to plant willows and cottonwoods for riparian restoration (Hoag 2007); Native shrubs and trees for riparian areas in the intermountain west (Tilley et al. 2012); and, Description, propagation, and establishment of wetland-riparian grass and grass-like species in the intermountain west (Hoag et al. 2011).

7. For all projects, sediment will be removed from erosion controls once the sediment has reached one-third of the exposed height of the control. If inspections show that the pollution controls are ineffective, the Project Sponsor will immediately mobilize work crews to repair, replace, or reinforce controls as necessary.

Re-watering Stream Channels. For stream channels which have been isolated and dewatered during project construction: (1) Reconstructed stream channels will be “pre-washed” into a reach equipped with sediment capture devices, prior to reintroduction of flow to the stream; and

(2) stream channels will be re-watered in a manner to minimize a sudden increase in turbidity.

Additional site-specific conservation recommendations should be employed as necessary to reduce the magnitude, frequency, and duration of turbidity plume events in excess of

50 nephelometric turbidity units (NTUs) over background levels. This may include, but may not be necessarily limited to:

Reducing…