Attach 3 ASIP Clear Creek Channel Phase 3B_0002.pdf

Action Specific Implementation Plan

Lower Clear Creek Floodway Rehabilitation Project – Phase 3B

JANUARY 2007

LEAD AGENCIES:

Northern California Area Office 16349 Shasta Dam Boulevard

Shasta Lake, CA 96019

6270 Parallel Road, Anderson, CA 96007 Redding Field Office

355 Hemsted Drive, Redding, CA 96002

Action Specific Implementation Plan, January, 2007 Lower Clear Creek Floodway Rehabilitation Project – Phase 3B

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TABLE OF CONTENTS

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List of Acronyms ...................................................................................................................................................iv Section 1 - Introduction Project Background Action Specific Implementation Plan Purpose Tiering from CALFED Programmatic Documents Coordination with Agencies Species Analyzed in this ASIP NCCP Communities Analyzed in this ASIP Covered Species and NCCP Community Goals Section 2 - Project Description Geographic Scope Purpose and Need Project Goals and Objectives Environmental Commitments Detailed Description of the Project Elements Contribution to MSCS Goals Section 3 - Approach to Assessment of Effects and Development of Conservation Measures to Avoid, Minimize, and Compensate for Effects Environmental Baseline Impact Mechanisms Methods to Assess Project-Related Effects Fish Wildlife Botanical Resources NCCP Community Characterization and Mapping Wetland Delineation Development of Conservation Measures CALFED Contribution to Species and Habitat Conservation Section 4 - Assessment of Project Effects on Covered Species and Conservation Measures Fish Sacramento River Winter-run Chinook Salmon Central Valley Fall-/Late Fall-run Chinook Salmon Central Valley Spring-run Chinook Salmon Central Valley Steelhead

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Hardhead Invertebrates Valley Elderberry Longhorn Beetle Amphibians and Reptiles Foothill Yellow-Legged Frog Northwestern Pond Turtle Birds Bald Eagle Bank Swallow Cooper’s Hawk Golden Eagle Little Willow Flycatcher Osprey Tricolored Blackbird Western Yellow-Billed Cuckoo Yellow-breasted Chat Yellow Warbler Mammals Ringtail Section 5 - Assessment of Project Effects on Natural Community Conservation Plan Communities and Conservation Measures Anadromous Fish Species Group Montane Riverine Aquatic Habitat Montane Riparian / Natural Seasonal Wetland Complex Valley / Foothill Woodland and Forest Section 6 - Assessment of Cumulative Interdependent and Interrelated Effects Cumulative Effects Interdependent and Interrelated Effects Section 7 - Adaptive Management Monitoring, Changed Circumstances, and Funding Section 8 - Project Monitoring Section 9 - Assurances Requested Section 10 - Alternatives to Take Considered and Rejected Anadromous Fish Valley Elderberry Longhorn Beetle Yellow-Breasted Chat and Yellow Warbler Section 11 - Determination of Effects

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Federal and State Listed Species Non-Listed Species Section 12 - References and Persons Consulted References Persons Consulted Section 13 - List of Participants

Figures Figure 1 - Site Vicinity Map Figure 2 - Project Location Map Figure 3A - Upstream Habitat Map Figure 3B - Downstream Habitat Map Figure 4 - Adaptive Management Framework

Appendices Appendix A - MSCS-Evaluated Species with Potential to Occur in the Restoration Project Area Appendix B - USFWS, NMFS, and DFG Species Lists Appendix C - ASIP-Addressed Special-Status Species Appendix D - Restoration Project Design Plans Appendix E - Restoration Project Conceptual Models Appendix F - Conservation Measure Monitoring Table

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LIST OF ACRONYMS

ACID Anderson-Cottonwood Irrigation District AFRP Anadromous Fish Restoration Program AMP Adaptive Management Plan AMPT Adaptive Management Planning Team ASIP Action Specific Implementation Plan BA Biological Assessment BLM U.S. Department of the Interior, Bureau of Land Management BMP Best Management Practices BO Biological Opinion CALFED CALFED Bay-Delta Program CALFED ROD CALFED Program Record of Decision CBDA California Bay Delta Authority CEQA California Environmental Quality Act CESA California Endangered Species Act CFS Cubic Feet per Second CNDDB California Natural Diversity Database CNFH Coleman National Fish Hatchery CNPS California Native Plant Society Conservation Agreement Conservation Agreement regarding the CALFED Bay-Delta Program Multi- Species Conservation Strategy Corps U.S. Army Corps of Engineers CRMP Coordinated Resource Management Planning Group CRR Cohort Replacement Rate CVP Central Valley Project CVPIA Central Valley Project Improvement Act CY Cubic Yards DDT Dichlorodiphenyltrichloroethane DFG California Department of Fish and Game DPS Distinct Population Segment DWR California Department of Water Resources EFH Essential Fish Habitat EIR Environmental Impact Report EIS Environmental Impact Study EPA U.S. Environmental Protection Agency ERP Ecosystem Restoration Program ESA Federal Endangered Species Act ESU Evolutionarily Significant Unit FMP Fishery Management Plan FR Federal Register GCID Glenn-Colusa Irrigation District GCS Grade Control Structures GIS Geographic Information Systems HCP Habitat Conservation Plan IFIM Instream Flow Incremental Methodology IS/EA Initial Study / Environmental Assessment LCCFRP Lower Clear Creek Floodway Rehabilitation Project

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MSA Magnuson-Stevens Fishery Conservation and Management Act MSCS Multi-Species Conservation Strategy NCCP Natural Community Conservation Plan NCCPA California Natural Community Conservation Planning Act NEPA National Environmental Policy Act NMFS National Marine Fisheries Service NMFS Programmatic BO National Marine Fisheries Service CALFED Bay-Delta Program Programmatic Biological Opinion NPDES National Pollutant Discharge Elimination System NPS National Park Service NRCS U.S. Department of Agriculture, Natural Resources Conservation Service NTU Nephelometric Turbidity Unit OSHA Occupational Safety and Health Administration / Act PCE Primary Constituent Elements PEIS/EIR CALFED Programmatic Environmental Impact Statement / Environmental Impact Report PL Public Law PRBO Point Reyes Bird Observatory Conservation Science Programmatic NCCP DFG’s Natural Community Conservation Planning Act Approval of the Determination CALFED Bay-Delta Program Multiple Species Conservation Strategy RBDD Red Bluff Diversion Dam Reclamation U.S. Department of the Interior, Bureau of Reclamation restoration project Lower Clear Creek Floodway Rehabilitation Project – Phase 3B restoration team Lower Clear Creek Restoration Team ROD Record of Decision RSP Rock Slope Protection RWQCB California Regional Water Quality Control Board SAM Spawning Area Mapping SPCCP Spill Prevention Control and Countermeasures Plan SRA Shaded Riverine Aquatic Sta Station SWP State Water Project SWPPP Storm Water Pollution Prevention Plan USC U.S. Code USFWS U.S. Fish and Wildlife Service USFWS Programmatic BO U.S. Fish and Wildlife Services CALFED Bay-Delta Program Programmatic Biological Opinion USGS U.S. Geological Survey VELB Valley Elderberry Longhorn Beetle VSP Viable Salmonid Population WIM Watershed Information Model WSE Water Surface Elevation WSRCD Western Shasta Resource Conservation District WUA Weighted Usable Area

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SECTION 1

INTRODUCTION

Project Background

The U.S. Department of the Interior Bureau of Reclamation (Reclamation), U.S. Department of the Interior Bureau of Land Management (BLM) and the Western Shasta Resource Conservation District (WSRCD), are working cooperatively to implement Phase 3B (restoration project) of the Lower Clear Creek Floodway Rehabilitation Project (LCCFRP). The restoration project is located on lower Clear Creek, southwest of Redding, in Shasta County, California (Figure 1).

The work is being conducted on behalf of the Lower Clear Creek Restoration Team (restoration team), made up of multiple federal, state and local agencies and stakeholders including Reclamation, BLM, U.S.

Fish and Wildlife Service (USFWS), U.S. Department of Agriculture Natural Resources Conservation Service (NRCS), California Department of Fish and Game (DFG), California Department of Water Resources (DWR), California Regional Water Quality Control Board (RWQCB), WSRCD and PRBO Conservation Science (PRBO). The LCCFRP is part of a larger, comprehensive lower Clear Creek watershed restoration program that includes spawning gravel augmentation, flow management, dam removal, erosion control, fuels reduction, and invasive weed management projects.

Several prior phases of the LCCFRP have been completed with Central Valley Project Improvement Act (CVPIA) and California Bay-Delta Authority (CBDA) Ecosystem Restoration Program (ERP) funding (Figure 2). Phase 1, funded by CVPIA, was completed in October 1998 and began removing material from the Reading Bar borrow site to isolate a large salmonid-stranding mining pit at the restoration site south pond complex. Phase 2A, funded by ERP and completed in 2000, continued the extraction of borrow material at the Reading Bar site to fill 18.4 acres of off-channel north bank mining pits, re-create floodplains, and revegetate floodplains. Extensive revegetation occurred at both the Reading Bar borrow site and the restoration site. Phase 2B, funded by ERP and completed in 2001, continued the floodplain restoration along the south bank and a portion of the downstream north bank, filling 59.5 acres of mining pits to eliminate the worst stranding sites. On-site borrow material was used, and floodplains were revegetated with native flora. Phase 3A, funded by ERP and completed in 2002, was the first project phase that involved relocation of the channel itself, which was moved from a channel lined with claypan into an area with deeper alluvium. Phase 3A included 12.9 acres of riparian revegetation on the newly constructed floodplains.

The two remaining sub-phases (3B and 3C) include extending the Phase 3A channel and floodplain restoration design downstream through the remaining 1.6 miles of impacted stream channel at the restoration site. WSRCD has received directed action funding from ERP to implement Phase 3B. Phase 3C is currently unfunded.

Reclamation and BLM are the federal co-lead agencies for compliance with the federal endangered species act (ESA) and the National Environmental Policy Act (NEPA). WSRCD is the state lead agency for compliance with the California Endangered Species Act (CESA) and the California Environmental Quality Act (CEQA). WSRCD is the lead agency for project management and acquiring environmental compliance authorizations including Clean Water Act Section 404 and Section 401, California Fish and Game Code Section 1603 and others, as required.

Action Specific Implementation Plan, January, 2007

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Action Specific Implementation Plan

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Action Specific Implementation Plan Purpose

This Action Specific Implementation Plan (ASIP) serves as the biological assessment (BA) for compliance with Section 7 of the ESA and the Natural Community Conservation Plan (NCCP) for compliance with CESA and the California Natural Community Conservation Planning Act (NCCPA).

The CALFED Programmatic Environmental Impact Statement/Environmental Impact Report Record of Decision (CALFED ROD) and the programmatic Multi-Species Conservation Strategy (MSCS) were used to identify special status species and natural communities that might be affected by the restoration project.

This ASIP presents information necessary for the following:

USFWS to issue incidental take authorization for the restoration project under Section 7 of the ESA for one species covered under the CALFED USFWS Programmatic Biological Opinion (BO), valley elderberry longhorn beetle (VELB) (Desmocerus californicus dimorphus);

USFWS to issue their concurrence with the determination that the restoration project is not likely to adversely affect one species covered under the CALFED USFWS Programmatic BO, bald eagle (Haliaeetus leucocephalus);

National Marine Fisheries Service (NMFS) to issue incidental take authorizations for the restoration project under Section 7 of the ESA for two Evolutionarily Significant Units (ESU) and one Distinct Population Segment (DPS) covered under the CALFED NMFS Programmatic BO, (Central Valley spring-run Chinook salmon ESU (Oncorhynchus tshawytscha), Sacramento River winter-run Chinook salmon ESU (Oncorhynchus tshawytscha) and Central Valley steelhead DPS (O. mykiss);

NMFS to issue conservation recommendations, pursuant to section 305 (b)(2) of the Magnuson- Stevens Fishery Conservation and Management Act (MSA), necessary to address potential adverse effects of the restoration project on Essential Fish Habitat (EFH) for three ESUs (Central Valley spring-run Chinook salmon ESU, Sacramento River winter-run Chinook salmon ESU and Central Valley fall/late fall-run Chinook salmon ESU (Oncorhynchus tshawytscha); and

DFG may, if required, issue incidental take authorization under Section 2835 of the NCCPA for species covered under the CALFED programmatic NCCP Determination.

Reclamation and BLM, as federal co-lead agencies for ESA compliance, request formal consultation and issuance of incidental take authorizations from USFWS and NMFS. WSRCD, as the state lead agency for CESA compliance, requests formal consultation and issuance of incidental take authorizations from DFG, where applicable and appropriate.

If an NCCP determination is required, the DFG will not require a separate implementation agreement since this ASIP binds the parties to their respective obligations and ensures that the restoration project is implemented in accordance with the MSCS.

The MSA, as amended, requires the identification of EFH and the implementation of measures to conserve and enhance habitat with a Fishery Management Plan (FMP), for Federally-managed fishery species that may be adversely affected by a federal action. EFH is defined as those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity. For the purpose of interpreting

Action Specific Implementation Plan, January, 2007 the definition of essential fish habitat, “waters” includes aquatic areas and their associated physical, chemical, and biological properties that are used by fish, and may include areas historically used by fish where appropriate; “substrate” includes sediment, hard bottom, structures underlying the waters, and associated biological communities; “necessary” means habitat required to support a sustainable fishery and a healthy ecosystem; and “spawning, breeding, feeding, or growth to maturity” covers all habitat types used by a species throughout its life cycle.

The restoration project is within the EFH of “Pacific salmon” which includes the Central Valley spring-run Chinook salmon ESU, the Sacramento River winter-run Chinook salmon ESU and the Central Valley fall/late fall-run Chinook salmon ESU. For this restoration project, the EFH assessment is integrated into the ASIP, and the EFH consultation process will be integrated into the NMFS Programmatic BO. The NMFS will provide EFH conservation recommendations for any action that may adversely affect EFH.

Tiering from CALFED Programmatic Documents

This project-specific ASIP tiers from the following five CALFED program-level compliance documents for ESA, CESA, and NCCPA.

Multi-Species Conservation Strategy (CALFED Bay-Delta Program 2000a), Programmatic Endangered Species Act Section 7 Biological Opinions on the CALFED Bay- Delta Program (USFWS 2000), CALFED Bay-Delta Program: Programmatic Biological Opinion and Essential Fish Habitat Conservation Recommendations (NMFS 2000a), Natural Community Conservation Plan Approval: California Department of Fish and Game Approval and Supporting Findings for the CALFED Bay Delta Program Multiple Species Conservation Strategy (DFG 2000), and

Conservation Agreement regarding the CALFED Bay-Delta Program Multi-Species Conservation Strategy (CALFED Bay-Delta Program 2000b).

These documents provide a broad, programmatic analysis of the general effects of implementing the CALFED plan over a 30-year period. Because of the broad nature of the MSCS, and the fact that it was not intended to address any environmental effects for site-specific projects, it is being incorporated by reference for purposes of background information and to demonstrate consistency with the overall CALFED plan.

Neither the programmatic biological opinions nor the programmatic NCCPA determination authorize take of MSCS evaluated species. This ASIP includes the necessary analysis of effects of the restoration project, including direct, indirect, cumulative and secondary effects, and provides conservation measure to avoid, minimize and compensate for impacts to MSCS evaluated species and NCCP communities.

Coordination with Agencies

The MSCS, and other program-level documents, require that CALFED project proponents, or lead agencies, coordinate preparation of ASIPs with CBDA, USFWS, NMFS, and DFG. This coordination between agencies serves to provide technical assistance regarding how adverse effects from the project

Action Specific Implementation Plan, January, 2007 can be avoided, minimized or mitigated through project design features, and the implementation of Best Management Practices (BMPs), conservation measures and mitigation.

Several informal consultation meetings regarding anadromous fish were held with Mr. Howard Brown of NMFS and Mr. Mike Berry of DFG during restoration team meetings and via phone calls and email communications between Mr. Brown, and Mr. Jeff Souza of Souza Environmental Solutions, Inc., Ms.

Patricia Bratcher of DFG, Mr. Michael Harris of WSRCD and Mr. Matt Brown of USFWS.

Several informal consultation meetings regarding the VELB were held on April 5, 2006 with Ms. Heidi Crowell, and on November 8, 2006 with Mr. Doug Powers of the USFWS Red Bluff Fish and Wildlife Office.

Informal consultation correspondence regarding migratory songbirds was held in February, 2006 between Mr. Bruce Deuel of DFG and Mr. Ryan Burnett of PRBO.

Consultations with NMFS, USFWS and DFG have occurred for prior phases of the LCCFRP under ESA, CESA and MSA. Consultations were conducted with NMFS and DFG for Phases 1, 2A and 2B.

Consultations were conducted with NMFS, USFWS and DFG for Phase 3A. The results of all of the above-referenced consultations concluded that the proposed actions would have no effect or were not likely to adversely affect listed or candidate species, their critical habitats or EFH.

Species Analyzed in this ASIP

Appendix A presents a list of all MSCS-evaluated special-status species and critical habitats that could potentially occur in the restoration project area. Appendix A also includes additional information for each species and critical habitat including legal and listing status, the MSCS species goal designation and an evaluation of the potential for occurrence within the restoration project area. The species list was compiled based on special-status lists provided by the USFWS, NMFS and DFG (Appendix B), and searches of the California Natural Diversity Database (CNDDB) (DFG 2006) and the California Native Plant Society (CNPS) Inventory of Rare and Endangered Plants (CNPS 2006) and personal communications with local biologists and botanists.

CALFED programmatic guidance documents require that effects of implementing CALFED projects on MSCS evaluated species and other special-status species that could be affected by a project must be assessed. This ASIP assesses the effects of the restoration project on MSCS-evaluated species that could occur in the restoration project area. An analysis of the potential affects of the restoration project on other special-status species that could occur within the restoration project area, but were not evaluated in the MSCS, is included in the joint CEQA Initial Study / NEPA Environmental Assessment (IS/EA) for the LCCFRP (Reclamation et al. 1999) and several subsequent IS addendums (WSRCD 2001) (WSRCD 2007, in press) and subsequent EAs (Reclamation and BLM 2001) (Reclamation and BLM 2006, in press).

Based on the list of potentially-occurring species found in Appendix A, information from a number of past field surveys, and personal communications with local biologists and botanists, a list of MSCS-evaluated species that may occur, are likely to occur, or are known to occur in the project area was compiled for inclusion in this ASIP (Appendix C).

Action Specific Implementation Plan, January, 2007

Three MSCS-evaluated species included in this ASIP are not covered under the programmatic BOs and NCCP Determination (foothill yellow-legged frog, golden eagle and hardhead). Because these species were not covered in the programmatic documents, incidental take under Section 7 of the ESA or Section 2835 of the NCCPA cannot be provided.

NCCP Communities Analyzed in this ASIP

The MSCS identified 20 NCCP communities which includes two ecologically-based fish groups and 18 habitats. This ASIP will address impacts of the restoration project on four NCCP habitats that are present in the restoration project area including Montane Riverine Aquatic, Natural Seasonal Wetland, Montane Riparian, and Valley/Foothill Woodland and Forest.

One of the MSCS-identified NCCP ecologically-based fish groups, Anadromous Fish Species, is present in the restoration project area and includes all of the covered anadromous fish species assessed in this ASIP including Sacramento River winter-run Chinook salmon, Central Valley spring-run Chinook salmon, Central Valley steelhead, and Central Valley fall/late-fall-run Chinook salmon.

Covered Species and NCCP Community Goals

The MSCS has established programmatic goals for each of the covered species and NCCP communities.

It is a collective commitment of CBDA to achieve the MSCS goals over the term of the programmatic BOs and NCCP determination. Relative to achieving these goals, some projects will not directly contribute to these goals, and some projects will be designed specifically to achieve these goals. All CALFED projects, however, must fully mitigate for project-related adverse effects on covered species and NCCP communities.

This restoration project is a CALFED ERP stream channel and floodway rehabilitation project and is designed specifically to help achieve MSCS goals for covered anadromous fish species, montane riverine aquatic habitat, montane riparian habitat and riparian-dependant wildlife species. The following project goals have been established for covered species and NCCP communities addressed in this ASIP:

Covered anadromous fish species: Avoid, minimize, and fully mitigate adverse effects of the restoration project on covered anadromous fish species and contribute to their recovery.

Other covered species: Avoid, minimize, and fully mitigate adverse effects of the restoration project on covered species.

Montane riverine aquatic habitat: Restore a natural stream channel and natural stream processes to create favorable habitat conditions for anadromous salmonids.

Montane riparian habitat: Restore functioning floodplain processes to create favorable habitat conditions for terrestrial wildlife species that are dependant on riparian habitats.

Action Specific Implementation Plan, January, 2007

SECTION 2

PROJECT DESCRIPTION

GEOGRAPHIC SCOPE

The watershed that forms Clear Creek begins in the Trinity Mountains at nearly 6,000 feet in elevation, and flows south between the Trinity River basin to the west and the Sacramento River basin to the east.

Upper Clear Creek flows into Whiskeytown Lake (elevation 1,210 feet), 11 miles west of Redding, California (Figure 1). The lower section of Clear Creek (lower Clear Creek) flows south from Whiskeytown Dam for approximately 8 miles, then east for 8 miles before joining the Sacramento River five miles south of Redding.

The restoration project is located on lower Clear Creek, approximately four miles upstream from the confluence with the Sacramento River, on public lands administered by BLM. Specifically, the restoration project is located between river mile 2.8 and river mile 4.3 in Sections 33 and 34, T.31N., R.5W., Mount Diablo Base & Meridian, within the 7.5-minute USGS Redding and Olinda quadrangle maps.

PURPOSE AND NEED

The restoration project is part of the larger multi-phased LCCFRP and is consistent with the purpose and need of the LCCFRP which is outlined below.

Purpose

The primary purpose of the LCCFRP is to rehabilitate salmon and steelhead habitats in a section of lower Clear Creek that has been severely degraded by gravel extraction activities and by blockage of bed load by Whiskeytown Dam. In addition, the LCCFRP is designed to restore ecological function to this degraded section of lower Clear Creek through rehabilitation of natural stream channel and floodplain morphology that is vegetated with diverse stands of native riparian plant species. Restoration of natural stream processes would allow Clear Creek to meander across floodplains creating favorable habitat conditions (pools and riffles) for anadromous salmonids while also providing diverse habitat conditions for various wildlife species that use riparian habitats for part or all of their life stages.

Need

The LCCFRP is driven by the needs of anadromous salmonids, primarily spring-run, fall/late fall-run Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss). Over the last 30 years, gravel extraction activities within the restoration site have removed the majority of the alluvial material that was once present throughout the stream channel and floodplain. The reach most impacted by gravel mining activities is approximately 8,000 feet in length and is located between river mile 2.2 and 3.8 (DWR 1986). This section has been mined extensively and contained several open gravel pits and numerous braided channels.

Removal of the alluvium lowered the stream channel, exposing hardpan and bedrock surfaces in many locations and has caused the stream channel to shallow and braid across the valley bottom. Adult salmon

Action Specific Implementation Plan, January, 2007 have difficulty passing through these shallow braided sections during periods of low flow. Furthermore, gravel mining activities created several large pits within the floodplain and braided stream channels known to trap adult and juvenile salmonids during periods of fluctuating flow. Salmonids that became trapped in these pits were vulnerable to higher water temperatures and become easy prey for predatory fish, birds and mammals. Reduced gravel supplies reduced the quality and quantity of valuable salmon spawning habitat available in the lower reaches of the creek.

Restoration of a functional single-thread channel and natural floodplain morphology would improve salmonid habitat conditions and greatly reduce stranding mortalities associated with degraded stream channel and floodplain conditions caused by gravel extraction activities. Rehabilitation of a functional bankfull channel that is free to meander across the floodplain would create diverse salmonid habitat conditions (pools, runs, and riffles) and would improve fish passage conditions for adult salmon migrating upstream during the fall and winter seasons. Restored floodplains would provide a continual source of new gravel and woody debris to the stream channel which in turn would increase habitat quality and diversity for rearing and spawning salmonids provided that the gravel and streamflow augmentation projects continue to be implemented in the future.

Riparian habitat along lower Clear Creek has been negatively impacted by gold dredging, gravel extraction, water diversion and flow regulation. These impacts include removal of riparian forest, alteration of floodplain morphology by mining activities, and encroachment of riparian vegetation into the low flow stream channel due to flow regulation. As a result, riparian berms and stringers have formed, which often lack habitat diversity. On floodplain surfaces, the existing riparian vegetation occurs between large tailing piles and other disturbed landscapes impacted by historic gold and gravel mining activities. Restoration of functional, frequently-flooded riparian habitats along lower Clear Creek would provide an increase in the quantity, quality and diversity of riparian habitat types and stages. Conversion of marginal upland habitats that are currently dominated by tailing piles to large diverse wetland habitats would greatly enhance wildlife values.

PROJECT GOALS AND OBJECTIVES

This restoration project will reconstruct the bankfull channel and portions of floodplain along approximately one mile of the LCCFRP restoration site in one construction season, restore riparian vegetation on the constructed floodplains and monitor the project for three years. The reconstructed bankfull channel is designed to function geomorphically within prior-constructed floodplain surfaces completed in earlier phases of the LCCFRP. The work will address a headcut (known as the Backbone reach) that has continued to migrate and is now threatening the successful channel and riparian habitat created in previous project phases. This headcut was documented and taken into account with the original design. However, it was anticipated that funding to complete the project would occur in a more timely manner given the identified importance of restoring lower Clear Creek. The downstream edge of the headcut has now migrated 700 feet upstream, and the low flow water surface elevation (WSE) in the upstream areas has already been dropped some 2.5 feet in recent years.

The overarching goal of the LCCFRP is to re-establish critical ecological functions, processes, and characteristics that best promote recovery and maintenance of resilient, naturally reproducing salmonid populations and the river’s natural animal and plant communities within the contemporary regulated flow and sediment conditions. This goal was developed by the restoration team, is supported by the lower Clear Creek Coordinated Resource Management Planning Group (CRMP), and is consistent with goals of the CBDA ERP, CVPIA, and the Anadromous Fish Restoration Program (AFRP).

Action Specific Implementation Plan, January, 2007

The objectives of the LCCFRP are to:

Rehabilitate the channel degraded by historic aggregate extraction at the restoration site by reconstructing the bankfull channel and floodplains.

Restore sediment transport processes, including coarse bedload transport continuity and fine sediment deposition on floodplain surfaces.

Restore native riparian vegetation on floodplain and terrace surfaces by focusing on species that provide a diverse canopy structure and removing competing exotic species.

Reduce salmonid stranding and mortality in floodplain gravel extraction pits.

Improve habitat conditions for native fish and wildlife species, including priority salmonid species of central concern to CALFED, CVPIA, and AFRP programs.

The objectives of the restoration project (Phase 3B of the LCCFRP) are to:

Re-establish an alternate bar morphology in the project area of the restoration site, including riffles, exposed gravel bars, and deep pools.

Design the channel dimensions to transport the channel bed particles at flows slightly less than the anticipated future channel-forming discharge (design discharge is 3,000 cubic feet per second [cfs]), allowing coarse sediment to route through the reach.

Design floodplains to begin inundation at flows slightly less than the design discharge, allowing fine sediments transported in suspension to deposit on floodplain surfaces.

Promote natural channel migration across the floodway during flows equal to or larger than the design discharge. Lateral channel movement is considered a success, not a failure.

Raise the bankfull channel thalweg at least three feet above clay hardpan to convert most of the channel bed back to a gravel and cobble surface.

Create micro-topography on reconstructed floodplains that simulates observed pre-dam high flow scour channels or abandoned primary channels to encourage natural regeneration of riparian vegetation. Revegetate constructed floodplains with native riparian vegetation.

Reduce the particle size in the design bankfull channel to optimize fish habitat by using appropriately-sized borrow materials.

ENVIRONMENTAL COMMITMENTS

The following environmental commitments will be implemented before and during implementation of the restoration project, where applicable. These measures are consistent with broader measures adopted in the CALFED ROD (CALFED Bay-Delta Program 2000c) and the MSCS.

Action Specific Implementation Plan, January, 2007

Contractor Environmental Education Program

Construction contractors, and all subcontractors, will be required to participate in, and fully comply with, an environmental education program. The program will include, but not be limited to, awareness training regarding: 1) federal, state, and local environmental laws and permits, as well as the penalties for non-compliance with environmental requirements and conditions, 2) threatened, endangered, and other special-status species, and their habitats, and 3) environmental protection measures, mitigation, compensation, and restoration. A member of the contractor’s management staff will be required to participate in the training session to discuss the contractor’s environmental protection plans.

Environmental Permits and Authorizations

WSRCD, BLM and Reclamation will obtain all applicable federal, state and local permits and authorizations for the implementation of the restoration project and will ensure that all conditions included in those permits and authorizations will be complied with. Where appropriate, the permit and authorization conditions will be incorporated into the construction plans and specifications. These permits and authorizations may include, but will not be limited to:

ESA, CESA, and the NCCP

California Fish and Game Code Section 1603 Lake and Streambed Alteration Agreement

Clean Water Act Section 404 Permit

Clean Water Act Section 401 Certification

National Pollution Discharge Elimination System (NPDES) Construction Storm Water and Dewatering Permits

Designated Work and Exclusion Zones

Construction equipment and activities will be confined to designated work zones including designated access roads. These work zones will be indicated on the project construction plans. Prior to construction, the work zones will be clearly flagged and staked. In addition, sensitive areas within, or near, the designated work zone will be indicated on the project plans as exclusion zones and clearly marked in the field with high-visibility fencing and/or flagging adequate to prevent accidental entry and maintained throughout construction activities.

Exclusion zones will have signs attached that identify each area as an Environmentally Sensitive Area.

The following paragraph will be included in the construction specifications for environmentally sensitive areas.

The contractor’s attention is directed to the areas designated as “Environmentally Sensitive Areas.” These areas are protected, and no entry by the contractor for any purpose will be allowed unless specifically authorized. The contractor shall take measures to ensure that the contractor’s employees and subcontractors do not enter or disturb these areas, including by issuing written notice to employees and subcontractors regarding compliance with restrictions for environmentally sensitive areas.

Action Specific Implementation Plan, January, 2007

During the environmental education program, construction personnel will be informed about the importance of working exclusively in designated work zones and the importance of avoiding any impacts to environmentally sensitive exclusion zones. During construction, job inspectors and resource monitors will ensure that construction equipment and ancillary activities avoid any disturbance of sensitive resources outside the designated work zones. Resource monitors will conduct surveys as appropriate for threatened, endangered, and special-status species. The following measures will also be implemented:

Use and storage of construction equipment will be confined to designated work zones.

Existing roads and access points will be used to the greatest extent possible to minimize disturbance to the environment and wildlife.

Equipment staging areas, borrow material sites, parking locations, stockpile areas, and storage areas will be located outside of Environmentally Sensitive Areas and will be clearly marked and monitored.

Fish Rescue Operation

A portion of the lower Clear Creek channel will be dewatered during construction activities, and dewatering may result in adult and juvenile fish becoming stranded. WSRCD and the USFWS, in coordination and consultation with the NMFS and the DFG, will ensure that fish biologists are on-site to implement fish rescue operations through the use of seining or electrofishing, if necessary. The potential feasibility of net blocking lower Clear Creek to prevent fish movement into the dewatered section of creek prior to cofferdam construction will be evaluated prior to dewatering activities. During dewatering, fish biologists will snorkel or dive in the impacted area to estimate the numbers and types of fish which may become stranded. Based on this information, best professional determination will be used to decide which method of rescue is most appropriate. Seining will initially be considered the most appropriate method of fish rescue and electrofishing discouraged to the greatest extent practicable as it can negatively impact fish and can lead to lethal take. If fish biologists determine that the use of electrofishing is necessary for the efficient and successful removal of fish, the NMFS electrofishing guidelines (NMFS 2000b) will be strictly followed. The fish rescue team will be comprised of qualified fishery biologist with professional experience using seines and electrofishing equipment.

The fishery biologist will use the following general rescue operation guidelines and will develop specific operation details in the field:

The teams will be comprised of 2-4 persons to facilitate efficient removal and rapid transport of fish from the dewatered area. Up to two fish rescue teams may be used to facilitate efficient fish removal, reduce handling time, lower physiological stress, and reduce potential mortality rates. If electrofishing is employed, a minimum of three passes through each stranding location will be conducted. Captured juvenile fish will be placed in 5-gallon buckets. At the end of each pass, captured fish will be transferred into buckets with aerated water or into in-river holding tanks (e.g., buckets with small holes allowing freshwater infiltration). After fish are fully recovered, they will be released to the main flowing lower Clear Creek channel. All captured adult fish will be placed in appropriately-sized containers and immediately transported and released to the main flowing lower Clear Creek channel. All rescued fish will be counted, measured, and recorded by species. The number and run-type of Chinook salmon and steelhead captured, and the number of fish accidentally killed prior to release, will be reported to NMFS and DFG.

Action Specific Implementation Plan, January, 2007

Environmental Timeframes

WSRCD will ensure that the contractor will complete all construction-related activities in a timely manner to minimize the duration of impacts to the environment and special-status species. In addition, all activities will occur at times of the year determined to be the least detrimental to the environment and special-status species. Through coordination with NMFS and DFG, all in-stream work is required to be conducted between June 1 and October 31 to minimize impacts to anadromous fish. Construction activities that could adversely affect nesting birds will be limited to a phased schedule between May 15 and December 1 that has been designed to minimize the potential for nesting occurrence. Sections 4 and 5 of this document include additional information about the conservation measures that will be implemented to avoid and minimize potentially adverse affects to sensitive species and NCCP natural communities.

Additional Environmental Commitments

In addition to the environmental commitments and constraints described above, WSRCD, BLM and Reclamation will obtain, develop, or adhere to the following:

Storm Water Pollution Prevention Plan Before construction begins, a Storm Water Pollution Prevention Plan (SWPPP) will be prepared in coordination with the RWQCB and other regulatory agencies. The SWPPP will include measures to minimize erosion and sediment transport to Clear Creek and will include the following, at a minimum:

Incorporation of BMPs such as sediment containment devices, protection of construction spoils, and proper installation of cofferdams

Post-construction site restoration

Contingency measures

Details about contractor responsibilities

A list or responsible parties

A list of agency contacts

Spill Prevention, Control and Countermeasures Plan Prior to construction, a spill prevention, control and countermeasures plan (SPCCP) will be prepared.

The SPCCP will include on-site handling rules to keep construction and hazardous materials out of waterways and drainages.

Riparian and Wetland Habitat Restoration Plan A riparian and wetland habitat restoration plan (North State Resources 1999a) was prepared for the LCCFRP which describes the conceptual methods for restoring riparian and wetland habitats. The plan also includes success criteria along with remedial measures in the event that the established success criteria are not met. The plan was reviewed and approved by the Corps prior to the implementation of Phase 2 of the LCCFRP as part of the issuance of a Clean Water Act Section 404 permit.

Specific riparian habitat designs have been prepared for each prior phase of the LCCFRP. Riparian habitat designs will be prepared for the restoration project after channel and floodplain construction

Action Specific Implementation Plan, January, 2007 activities are completed and a site assessment is completed to provide information about subsurface soil and groundwater conditions.

Migratory Bird Treaty Act Mitigation and conservation measures that will be implemented for the protection of special-status bird species are also expected to minimized impacts to other migratory bird species protected under the Migratory Bird Treaty Act. Section 4 of this document contains additional information regarding potential affects of the restoration project on, and conservation measures for, specific migratory bird species.

Project Monitoring Components The restoration project will have two monitoring components, including:

monitoring prior to, and during, construction to ensure that conservation measures and BMPs are implemented post-construction adaptive management monitoring to assess the effectiveness of the restoration project relative to the vegetation, geomorphic, fisheries and avian success criteria established in the Ecological Monitoring Plan (WSRCD 2005a) for the LCCFRP. Details of these monitoring components are found in Sections 7 and 8 of this document.

DETAILED DESCRIPTION OF THE PROJECT ELEMENTS

Project Design

The restoration project will continue the restoration work that was previously completed during prior phases of the LCCFRP, which started in 1998. The design plans for the restoration project are included as Appendix D. The design involves site grading to restore a natural floodplain surfaces that will periodically inundate under the contemporary flow regime, moving the current stream channel to a new location off of clay bedrock, and backfilling the new channel with several feet of clean spawning gravel.

The work will occur at three sites including the upstream Northstate Bar borrow area (borrow area), the Phase 2A project area and the Phase 3B project area. Specific heavy equipment construction methods will be left up to the contractor selected to perform the work, but it is likely that dozers, loaders, scrapers, excavators, backhoes, trenchers and dump trucks will be used.

The designs call for a cut and fill of material composed of excavated floodplain material from the borrow area and clean spawning gravel that will be imported from commercial aggregate sources. Approximately 62,000 cubic yards (CY) of net cut material will be exchanged for clean spawning gravel for the project.

The spawning gravel will meet standard specifications that are regularly used for spawning gravel augmentation projects. The spawning gravel will come from off-stream sources, will be 1-inch to 4-inch (or as determined appropriate by the restoration team) rounded river rock, will be washed at least once and will have a cleanness value of 85 or higher (CALTRANS Test No. 227). BMPs will be used to control erosion and meet water quality objectives.

The restored floodplain surfaces will include scour channels that are designed to provide topographic diversity, encourage the natural regeneration of riparian vegetation and create edgewater/ backwater areas for juvenile salmonid rearing habitat. The scour channel design includes a V-notch center that is designed as a drainage feature to alleviate potential juvenile salmonid stranding. Several areas of high-quality riparian habitat within the floodplain contruction areas will be retained as wildlife habitat and to

Action Specific Implementation Plan, January, 2007 provide seed sources for natural establishment of riparian vegetation. The elevation of several previously-constructed floodplain surfaces will be lowered to make the areas more favorable for the establishment of riparian vegetation.

The construction of the new creek channel will require the diversion of flows into several constructed bypass channels to dewater the construction areas. Once the future channel is constructed, flows will be diverted from the bypass channels into the new creek channel. The bypass channels will then be filled to become floodplains or will be modified to act as scour channels. All channel dewatering will occur over an extended period of time to minimize water quality impacts downstream of the project and to encourage any existing adult or juvenile salmonids to leave the dewatered area as the water temperatures gradually increase. USFWS staff will monitor the dewatered areas daily to ensure that as many adult or juvenile fish have moved out of the area as possible prior to blocking the downstream connection to the main channel and proceeding with fish rescue operations, if needed. Upon completion of any necessary fish rescue operations, construction activities will proceed in the dewatered areas.

Three temporary stream crossings will be installed to allow equipment to access both the north and south sides of lower Clear Creek. The contractor will be given the option to construct the crossing using culverts or a portable bridge. If a bridge is used, the bottom of the bridge will be set a minimum of two feet above the 250 cfs WSE. If culverts are used, the crossings will be constructed using designs that meet the NMFS fish passage guidelines (NMFS 2001). The two alternative designs for the stream crossings are included on Sheet 2 of the design plans in Appendix D. Upon completion of construction, the crossings will be removed and any spawning gravel used in the construction will be spread into the channel and left in place.

Several buried rock grade control structures (GCS) and one biotechnical bank protection structure will be installed to keep lower Clear Creek from reoccupying the former channel location (Appendix D, Sheet 5).

The GCS at the downstream end of the project would eventually be removed during the final phase of work (Phase 3C), if implemented. The biotechnical bank protection structure will utilize logs with, and without, attached rootwads. Some of the logs will come from trees that are removed during project clearing and grubbing activities. Additional logs will be imported by the contractor from undetermined source areas. The logs will be pinned together and secured using paired boulders that are cabled together.

Several log fish habitat structures will also be installed along the margins of the new creek channel and secured in a similar manner as the biotechnical bank protection structure. One rock slope protection (RSP) structure will be installed to stabilize an existing eroding bank near the biotechnical bank protection structure.

After completion of the earthwork, the new floodplain surfaces will be revegetated with native woody species. The emphasis will be on creating riparian habitat, where site conditions are favorable. The revegetation designs will be similar to those implemented in past phases which involved the planting of hardwood cutting of Fremont cottonwood (Populus fremontii) and several species of willows into…