Biological and Conference Opinion on the Lower Colorado River Multi-Species Conservation Program, Arizona, California, and Nevada
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United States Department of the Interior U.S. Fish and Wildlife Service 2321 West Royal Palm Road, Suite 103 Phoenix, Arizona 85021-4951 Telephone: (602) 242-0210 FAX: (602) 242-2513 In Reply Refer To: AESO/SE 02-21-04-F-0161 March 4, 2005 Memorandum To: Regional Director, Southwest Region, Fish and Wildlife Service, Albuquerque, New Mexico (ARD-ES) Regional Director, Lower Colorado Region, Bureau of Reclamation, Boulder City, Nevada (LC1200 ENV-1.10) From: Field Supervisor Subject: Biological and Conference Opinion on the Lower Colorado River Multi-Species Conservation Program, Arizona, California, and Nevada This memorandum constitutes the attached biological and conference opinion (BCO) for the Lower Colorado River Multi-Species Conservation Program (LCR MSCP). This BCO addresses the effects to 27 species for which six Federal agencies and 24 Permit Applicants from Arizona, California, and Nevada requested incidental take coverage under section 7 and section 10 of the Endangered Species Act. The BCO determined that the proposed actions described herein are not likely to jeopardize the continued existence of listed, candidate, or other covered species, and are not likely to destroy or adversely modify designated or proposed critical habitat. Because this document is lengthy with many sections, we have provided a table of contents to assist in locating specific areas of the BCO. The official signature page for this BCO is located after the Reinitiation Notice on page 138. We appreciate the efforts of the staff at the Bureau of Reclamation and the Southwest Regional Office of the Fish and Wildlife Service in preparing this document. If there are any questions concerning this BCO, please contact Jeff Whitney, Lesley Fitzpatrick, or me. 2 BIOLOGICAL AND CONFERENCE OPINION FOR THE LOWER COLORADO RIVER MULTI-SPECIES CONSERVATION PROGRAM TABLE OF CONTENTS Introduction 6 Consultation History Relevant Previous Consultations and Development of the LCR MSCP 11 Current Consultation 13 Biological Opinion 15 Description of the Proposed Actions Federal Agency Actions Reclamation Actions 18 Western’s Actions 22 BIA Actions 22 BLM Actions 24 FWS Actions 24 NPS Actions 25 Implementation of the Conservation Plan 25 Non-Federal Covered Actions Arizona 28 California 29 Nevada 30 Amounts and Types of Incidental Take Flow-Related Incidental Take 31 Non-Flow Related Incidental Take (Footprint Actions) 34 Other Non-Flow Related Incidental Take (Continuing Actions) 35 Incidental Take Related to Creation of Restoration Sites 38 Incidental Take Resulting from Harassment 41 Incidental Take Due to Water Operations 41 Incidental Take Resulting Effects of On-Going Actions 44 Status of the Species Rangewide Listed Species Yuma clapper rail 44 Southwestern willow flycatcher 46 Desert tortoise 48 Bonytail 50 Humpback chub 52 Razorback sucker 55 Other Covered Species 59 Environmental Baseline Definition of the Action Area 60 Environmental Baseline for the LCR MSCP Planning Area 3 Pre-development conditions (pre-1880) 63 Existing conditions 67 Section 7 consultations on the LCR since April 2002 78 Future conditions 78 Status of the Listed Species in the Action Area Yuma clapper rail 80 Southwestern willow flycatcher 83 Desert tortoise 86 Bonytail 87 Humpback chub 90 Razorback sucker 91 Status of the Other Covered Species in the Action Area 98 Effects of the Action Direct and Indirect Effects of Completed Actions Related to the Proposed Action 99 Direct and Indirect Effects of Proposed Actions that are Continuing Actions 100 Direct and Indirect Effects of Future Actions in the Action Area Reclamation Actions 103 BIA Actions 107 FWS and BLM Actions 108 NPS Actions 108 Actions Associated with Hydropower Generation 109 State Covered Actions 111 Direct and Indirect Effects of Implementing the Conservation Plan 111 Direct and Indirect Effects of Issuing a Section 10(a)(1)(B) Permit Yuma clapper rail 113 Southwestern willow flycatcher 113 Desert tortoise 114 Bonytail 115 Humpback chub 115 Razorback sucker 116 Direct and Indirect Effects to Critical Habitat Southwestern willow flycatcher 117 Desert tortoise 119 Bonytail 120 Razorback sucker 122 Interrelated and Interdependent Activities 125 Indirect Effects Outside the Action Area 125 Cumulative Effects 128 Conclusion Yuma clapper rail 130 Southwestern willow flycatcher 131 Desert tortoise 131 4 Bonytail 132 Humpback chub 133 Razorback sucker 133 Other covered species 134 Incidental Take Statement 135 Amount or Extent of Take Anticipated 136 Effect of the Take 136 Reasonable and Prudent Measures 136 Minimization and Mitigation to the Maximum Extent Practicable 137 Disposition of Dead or Injured Listed Animals 137 Conservation Recommendations 138 Reinitiation Notice 138 Literature Cited 140 Personal Communications 157 Tables Table 1: Section 10(a)(1)(B) Permit Applicants 8 Table 2: Quantified incidental take in acres and miles of river resulting from habitat loss due to implementation of the Federal and non-Federal covered actions 32 Table 3: Extent of existing and new facilities that will require maintenance activities over the life of the consultation and permit 36 Table 4: Number of Yuma clapper rails recorded during surveys, 2000-2004, on the LCR and showing relevant percentages in relation to total birds surveyed and to birds surveyed on LCR 81 Figures Figure 1: LCR MSCP Planning Area 16 Figure 2: Yellow-Billed Cuckoo Western Population Distribution 183 Figure 3: Previous Modeling: Lake Mead End-of-December Water Elevations 213 Figure 4: New Modeling: Lake Mead End-of-December Water Elevations 214 5 Appendices Appendix A: List of Acronyms 159 Appendix B: Concurrence for Bald Eagle 161 Appendix C: Jeopardy/Adverse Modification Biological Opinions 163 Appendix D: Rangewide and LCR MSCP Planning Area Status, Effects of the Action, and Conservation Measures for Unlisted Covered Species 165 Appendix E: Significant Section 7 Consultations Involving the LCR MSCP Planning Area, April 2002 –Present 210 Appendix F: Lake Mead End-of-December Water Elevations—Comparison of Baseline to Action Alternative Conditions 213 6 INTRODUCTION This biological and conference opinion (BCO) responds to the Fish and Wildlife Service (FWS) requirement for intra-Service consultation on the issuance of a section 10(a)(1)(B) permit pursuant to section 7 of the Endangered Species Act of 1973, as amended (16 U.S.C. 1531 et seq) (Act), for the Lower Colorado River Multi-Species Conservation Program (LCR MSCP). The permit application was certified as complete on June 9, 2004, and was officially transmitted by the Arizona Ecological Services Office (AESO) to the FWS Regional Office in Albuquerque, New Mexico. This BCO also responds to the Bureau of Reclamation’s (Reclamation’s) November 29, 2004, request for formal consultation with the FWS for the actions of six Federal agencies on the lower Colorado River (LCR) and the implementation through Reclamation of the LCR MSCP Conservation Plan. The LCR MSCP planning area is defined by the LCR and its historical floodplain from the full pool elevation of Lake Mead in the Grand Canyon to the Southerly International Boundary (SIB) with Mexico and includes portions of Mohave, La Paz, and Yuma counties in Arizona; San Bernardino, Riverside, and Imperial counties in California; and Clark County, Nevada. The FWS worked closely with the LCR MSCP Federal and non-Federal participants to develop the Habitat Conservation Plan (HCP) and other documents. On April 16, 2004, the AESO received the permit application and the LCR MSCP planning documents, all dated April 14, 2004, consisting of a draft HCP containing the Conservation Plan (LCR MSCP 2004a), a draft Biological Assessment (BA) for the Federal actions (LCR MSCP 2004b), a draft Environmental Impact Statement/Environmental Impact Report (EIS/EIR) (U.S. Department of Interior [USDOI] and The Metropolitan Water District of Southern California [Metropolitan] 2004a), and a separate volume of appendices (LCR MSCP 2004c). The LCR MSCP Conservation Plan (Conservation Plan) was described and included as the proposed action in both the draft BA and draft HCP. Minor modifications were made to the April 14, 2004, versions of these documents during the initial processing period. Versions of the documents dated June 18, 2004 (LCR MSCP 2004d, 2004e, 2004f; USDOI and Metropolitan 2004b), were provided to the public for review. Comments were received and considered in preparation of the final versions of the documents, which are dated December 17, 2004, (LCR MSCP 2004g, 2004h, 2004i, 2004j; USDOI and Metropolitan 2004c). We also used the updated river modeling contained in the “Evaluation of Effects Associated with Updated Hydrologic Information” (USBR 2004), which is contained in the appendices document (LCR MSCP 2004h). We used the information in the final versions of the LCR MSCP documents in our evaluation of the two Federal actions considered in this BCO: (1) the issuance of a section 10(a)(1)(B) permit by the FWS; and (2) specified actions of the other Federal agencies (with Reclamation as the lead agency for the consultation) including implementation of the Conservation Plan through Reclamation. The focus of our evaluation is to ensure that all Federal actions considered in this consultation do not appreciably reduce the likelihood of survival and recovery of the covered species, do not destroy or adversely modify proposed or designated critical habitat, and that the conservation plan minimizes and mitigates the effects of incidental take to the maximum extent practicable.