BIOLOGICAL/CONFERENCE OPINION REGARDING THE EFFECTS OF OPERATION OF THE U.S. BUREAU OF RECLAMATION’S PROPOSED 10-YEAR OPERATION PLAN FOR THE KLAMATH PROJECT AND ITS EFFECT ON THE ENDANGERED LOST RIVER SUCKER (Delistes luxatus) ENDANGERED SHORTNOSE SUCKER (Chasmistes brevirostris) THREATENED BALD EAGLE (Haliaeetus leucocephalus) AND PROPOSED CRITICAL HABITAT FOR THE LOST RIVER AND SHORTNOSE SUCKERS Prepared by the U.S. Fish and Wildlife Service Klamath Falls Fish and Wildlife Office Klamath Falls, Oregon Regional Director, Bureau of Reclamation Biological Opinion (1-10-02-F-121) Regional Director, Bureau of Reclamation Biological Opinion (1-10-02-F-121) EXECUTIVE SUMMARY INTRODUCTION This jeopardy biological opinion (BO) and conference report addresses the effects of operation of the Bureau of Reclamation’s (Reclamation) Klamath Project (Project) from June 1, 2002, through March 31, 2012, on the endangered Lost River sucker (LRS), endangered shortnose sucker (SNS), threatened bald eagle, and proposed critical habitat for the LRS and SNS (collectively suckers). The Project delivers water to about 220,000 acres of irrigated agriculture in the upper Klamath River Basin (Basin) in south-central Oregon (Klamath County) and northern California (Modoc and Siskiyou counties), as well as to the Tule Lake and Lower Klamath National Wildlife Refuges (NWRs). The Project consists of three main reservoirs with a total surface area of about 100,000 acres, many miles of canals and ditches, and numerous water control structures, pumps, and other structures. Related to the proposed action is operation of PacifiCorp’s hydroelectric facilities on the Link River and the Klamath River, and New Earth Corporation’s algae harvest facility at the “C-drop” off of the A-canal. Summary of Recent Consultation History Three principal actions occurred prior to the development of this final BO: (1) the Service issued an April 5, 2001, BO on Reclamation’s proposed operation of the Project from April 2001 to April 2002; (2) in January 2002, the National Academy of Sciences’ (NAS) Committee on Endangered and Threatened Fishes in the Klamath River Basin issued an Interim Report that contains an analysis of the Service’s 2001 BO; and (3) on March 28, 2002, the Service issued a non-jeopardy BO regarding Reclamation’s proposed operation of the Project during April and May 2002. The primary differences between the 2001 consultation and the 2002 consultation on operation of the Project are: (1) the 2001 BO addressed a one year operation plan for the Project during a critically dry inflow year type, while; the 2002 BO addresses a ten-year operation plan for the Project covering all water year types; (2) the 2002 BO considers additional information from the Interim Report of the National Academy of Sciences and comments from other peer reviewers; (3) the 2002 BO considers new information on the factors contributing to catastrophic fish die-offs; and (4) the 2002 BO is based on Reclamation’s proposed action that provides for fish screening and fish passage structures that have been required as a result of previous consultations since 1992, and involves water management at Upper Klamath Lake (UKL) based on the hydrograph for the 10-year period from 1990 to 1999, which poses less risk to the suckers and is consistent with recommendations in the Interim Report prepared by the NAS. The findings reported by the NAS Committee on Endangered and Threatened Fishes in the Klamath River Basin in their January 2002 Interim Report are largely in agreement with the Service’s findings in its 2001 BO. The Interim Report concluded that there is no clear empirical evidence for a relationship between lake levels and catastrophic die-offs of the two sucker species in UKL. In reference to the 2001 BA, the committee found: “At the same time the committee concludes that there is no scientific basis for operating the lake at mean minimum levels below the recent historical ones (1990-2000), as would be allowed under the USBR proposal. Operations leading to lower lake levels would require acceptance of undocumented risk to the suckers.” (NRC 2002). The Service agrees that this relationship is complex and not completely understood. However, the Service has established -i- Regional Director, Bureau of Reclamation Biological Opinion (1-10-02-F-121) relationships between lake level and crucial conservation needs of the two endangered suckers based on the best available scientific information, including: sucker access to foraging, refuge, and spawning habitat; and effect of lake level on factors that affect water quality conditions including algae growth . The benefits associated with lake levels that provide for the conservation needs of the suckers additively improve the “welfare” or condition of the suckers or contribute to or mitigate conditions that adversely impact their welfare. In conformance with the findings and conclusions of the Interim Report, the Service agrees that the 10-year operation plan proposed for the Project by Reclamation in their Biological Assessment (BA) will result in the maintenance of a mean lake level at UKL of approximately 4139 ft over time. Despite the lack of an empirical correlation between lake level and sucker welfare, the BO discusses the best available scientific information supporting a relationship between lake level (as it relates to water depth, which is the factor affecting water quality) and factors that affect water quality, which directly impacts sucker health and survival. Acknowledging evidence that water levels directly or indirectly affect factors that affect water quality, and that water quality impacts suckers, is not contrary to the NAS Interim Report. Additionally, certain lake levels allow adult sucker access to spawning sites and water-quality refuge areas, and provided juvenile suckers with access to emergent vegetation and gravel, rearing habitats, both of which enhance species survival. The Service will review the final NAS report and will request reinitiation of formal consultation on the Project, if appropriate. New information, that gives preliminary evidence of trends, indicates that high runoff caused by winter/spring storm events, which flush larger than normal quantities of organics and nutrients into UKL, may trigger adverse water quality conditions leading to sucker die-offs later in summer. Thus, although adequate inflow into UKL remains important to the welfare of the suckers, studies suggest that other factors also need to be considered and eventually offset. Adaptive management is an important process that can help to address such factors and, for that reason, is part of the Reasonable and Prudent Alternative provided under this BO to remove the jeopardizing effects of Reclamation’s proposed action. On April 25, 2002, the Service issued a draft jeopardy opinion to Reclamation. There was a public comment period on the draft opinion from April 25 to May 10, 2002. On May 13, 2002, Reclamation formally transmitted comments on the draft opinion to the Service; a total of 487 comments from 22 sources were provided by Reclamation. These comments were reviewed and considered by the Service in preparing this document. Our specific responses to Reclamation’s comments and those submitted by the State of California, the Klamath Tribes, and PacifiCorp are provided in Appendix H. A copy of all comments received by Reclamation and our responses to those comments are on file at the Klamath Falls Fish and Wildlife Office. Appropriate changes have been made within the text of this document in response to these comments. LIFE HISTORY AND ENVIRONMENTAL BASELINE Sucker Biology. The LRS and SNS are endemic to the Basin. The three major Project reservoirs (UKL, Clear Lake, and Gerber Reservoir) represent their primary habitats, with UKL representing the principle populations of both species. Tule Lake once supported a large population of suckers but habitat conditions there are now so degraded that only a few hundred suckers remain. Sucker populations in Clear Lake and Gerber Reservoir, although not well studied, appear relatively stable, but their population viability is at risk from reductions in water depth, adverse water quality, and lack of -ii- Regional Director, Bureau of Reclamation Biological Opinion (1-10-02-F-121) access to spawning areas. Sucker populations in UKL are at risk of extirpation from adverse water quality, loss of habitat, entrainment, and lack of passage. Environmental Baseline. The environmental baseline for the suckers is characterized by degraded aquatic ecosystems throughout the Basin. The baseline has been adversely affected over the past 150 years by agriculture, grazing, forestry, and to a smaller degree, urbanization. Project effects occur throughout the entire range of both the LRS and SNS and have been a major factor in contributing to the loss or degradation of aquatic habitats in the Basin and the endangered status of the two suckers. Nearly all Basin streams and rivers have been degraded, some seriously, by the loss of riparian vegetation, geomorphic changes, introduction of return flows from agricultural drainage ditches and water pumped from drained wetlands, stream channelization, dams, and flow reductions from agricultural and hydroelectric diversions. Most water bodies in the Basin fail to meet state water quality criteria. Wetland losses have been especially significant for suckers since wetlands provide habitat for larval and juvenile suckers and have crucial water quality functions. Along the perimeter of UKL, about 40,000 acres of wetlands have been diked and drained for agriculture; elsewhere in the Basin, wetland losses are even larger. Lower Klamath and Tule Lakes no longer support suckers or have been reduced to a few hundred acres of suitable habitat. Restoration of wetland and riparian habitats has been initiated throughout the Basin on private and public lands. In addition, Total Maximum Daily Loads (TMDLs) are being developed to address water quality. Adequate compliance with Clean Water Act requirements combined with habitat restoration should result in water quality and habitat improvements and will reduce threats and contribute to the conservation of the suckers.