United States Department of the Interior U.S. Fish and Wildlife Service Arizona Ecological Services Office 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 22410-2011-F-0100 22410-2011-F-0112 December 23, 2011 Memorandum To: Regional Director, Bureau of Reclamation, Salt Lake City, Utah From: Field Supervisor Subject: Final Biological Opinion on the Operation of Glen Canyon Dam including High Flow Experiments and Non-Native Fish Control Thank you for your request for formal consultation with the U.S. Fish and Wildlife Service (FWS) pursuant to section 7 of the Endangered Species Act of 1973 (16 U.S.C. 1531-1544), as amended (ESA). Your January 2011 request was supplemented with Biological Assessment (BA) dated July 13, 2011, and received by us on July 15, with supplements provided as described in the Consultation History section of this document. At issue are impacts that may result from the proposed 10-year continued operation of Glen Canyon Dam under the Modified Low Fluctuating Flows (MLFF) alternative along with High Flow Experimental (HFE) Releases and Non-Native Fish (NNFC) Control downstream from Glen Canyon Dam (GCD), Coconino County, Arizona. The Bureau of Reclamation (Reclamation) concluded that the proposed action “may affect, and is likely to adversely affect” the humpback chub (Gila cypha) and its critical habitat, the razorback sucker (Xyrauchen texanus) and its critical habitat, and the Kanab ambersnail (Oxyloma kanabensis haydenii). You also concluded that the proposed action “may affect, but is not likely to adversely affect” the southwestern willow flycatcher (Empidonax traillii extimus). We concur with your determination on the flycatcher and provide our rationale in Appendix A. This biological opinion (Opinion) replaces the 2008 Final Biological Opinion on the Operation of Glen Canyon Dam (USFWS 2008a, consultation number 22410-1993-F-R1 and the court ordered supplements to that opinion). This Opinion is based on information provided in Reclamation’s January and July BAs biological assessments on HFE Releases and NNFC, the draft environmental assessment on HFE Releases and NNFC, telephone conversations and meetings between our staff, and other sources of information found in the administrative record supporting this Opinion. All other aspects of the proposed action remain the same as described in the Environmental Assessments (EA) and BAs. Literature cited in this biological opinion is not a complete bibliography of all literature available on the species of concern. A complete 2 administrative record of this consultation is on file at this office. The proposed action is the continued operation of Glen Canyon Dam under MLFF with the inclusion of a protocol for high- flow experimental releases from Glen Canyon Dam and non-native fish control for the 10-year period, 2011 through 2020. It is the FWS's biological opinion that the action, as proposed, is not likely to jeopardize the continued existence of the humpback chub, razorback sucker, or Kanab ambersnail and is not likely to destroy or adversely modify designated critical habitat for razorback sucker or humpback chub. A Table of Contents is provided below. Table of Contents CONSULTATION HISTORY ....................................................................................................... 3 DESCRIPTION OF THE PROPOSED ACTION .......................................................................... 5 TABLE 1. GLEN CANYON DAM RELEASE CONSTRAINTS AS DEFINED BY RECLAMATION IN THE 1996 RECORD OF DECISION (RECLAMATION 1996). ............. 10 ENVIRONMENTAL BASELINE............................................................................................ 40 A. Status of the species and critical habitat within the action area .................................... 42 B. Factors affecting species’ environment within the action area ..................................... 73 EFFECTS OF THE ACTION ................................................................................................... 76 CUMULATIVE EFFECTS ...................................................................................................... 98 CONCLUSION ............................................................................................................................. 99 AMOUNT OR EXTENT OF TAKE .......................................................................................... 110 EFFECT OF THE TAKE............................................................................................................ 112 3 Consultation history January 14, 2011 Reclamation submitted a BA and requested initiation of formal consultation on the Development and Implementation of a Protocol for High-Flow Experimental Releases from Glen Canyon Dam, Arizona, 2011-2020. January 28, 2011 Reclamation submitted a BA, Draft EA, and requested informal consultation on implementation of Non-native Fish Control downstream from Glen Canyon Dam, Arizona, 2011-2020. March 17, 2011 FWS submitted separate comments for the following: Draft EA for Development and Implementation of a Protocol for High-Flow Experimental Releases from Glen Canyon Dam (HFE Protocol), Arizona, 2011-2020; and Draft EA for Non-native Fish Control Downstream from Glen Canyon Dam (Non-native Fish Control). These reviews provided input on biological analysis and conservation needs for humpback chub, non-listed native species, and other fish and wildlife resources. June 6, 2011 The FWS provided additional comments (email memorandum) for continuing issues to be addressed. July 18, 2011 Reclamation submitted a Supplement to the BA responding to input received from, among others, FWS (as described above), and requested that the proposed action be modified to include: 1. A fuller description clarifying baseline operations that would form the basis for HFE implementation (the MLFF alternative as described in the 1995 Environmental Impact Statement and adopted in the 1996 ROD) for the 10-year period from 2011-2020. 2. Non-native fish control in the Little Colorado River (LCR) reach only when the number of adult humpback chub falls below 7,000. 3. A request that the proposed HFE protocol, non-native fish control (two separate BAs), and continued ROD operations (2011-2020) be evaluated in a single biological opinion. July 26, 2011 - FWS sent a memo to Reclamation acknowledging the request for the modified proposed action (re: non-native fish control), and the request for a single biological opinion and expedited consultation. 4 August 24, 2011 and August 25, 2011 Informal meetings between Reclamation and the FWS in Phoenix, Arizona concerning the BAs for Non-native Control and High Flow Experiment. Notes compiled by Reclamation staff. August 31, 2011 Conference call between Reclamation and FWS with notes by Reclamation staff. September 2, 2011 Conference call between Reclamation, FWS, National Park Service (NPS), and Grand Canyon Monitoring and Research Center (GCMRC) to discuss the scientific merits of some potential changes to the proposed action. September 6 - 8, 2011 FWS participated in the National Historic Preservation Act Section 106 Meeting in Phoenix along with Federal, State, Tribal, and private partners. FWS staffs discuss with meeting attendees the ongoing section 7 consultation. October 4, 2011 Reclamation and FWS agree to general conservation measures for the draft biological opinion. Reclamation requests final Opinion by the end of November. October 27, 2011 Reclamation sent revised Conservation Measures to FWS. November 8, 2011 and November 18, 2011 Conference calls with DOI, Reclamation, and FWS to review status of draft Opinion. Some revisions of conservation measures were provided. November 25, 2011 FWS sent draft biological opinion to Reclamation for agency review. November 30, 2011 Reclamation provides comments on the draft Opinion and requests review of a second draft. December 6, 2011 Second revised draft Opinion provided to Reclamation for review. December 8, 2011 Reclamation responded to second draft Opinion. 5 December 14, 2011 Third draft Opinion provided to Reclamation for review. December 20, 2011 Conference call between FWS and Reclamation. Reclamation provides comments on the third draft document. December 21, 2011 and December 22, 2011 Reclamation and FWS discuss final draft biological opinion. BIOLOGICAL OPINION DESCRIPTION OF THE PROPOSED ACTION The proposed action is the continued operation of Glen Canyon Dam under MLFF with the inclusion of a protocol for high-flow experimental releases from Glen Canyon Dam and non- native fish control for the 10-year period, 2011 through 2020. The 10-year period for the proposed action is based on the experimental development of the high-flow protocol, allowing a sufficient period of time to assess the long-term effects of repeated high-flow releases as a potential action to benefit downstream resources. The Department is also undertaking an Environmental Impact Statement (EIS) process to evaluate the Long-Term Experimental and Management Plan (LTEMP) which will be addressed as a separate Federal action. HFEs The proposed action is intended to meet the need for high-flow experimental releases during limited periods of the year when large amounts of sand from tributary inputs are likely to have accumulated in the channel of the Colorado River. HFEs restore sand bars in Grand Canyon which are thought to provide backwaters that are beneficial to humpback chub. Annual and