Joint Biological Assessment
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Joint Biological Assessment Bureau of Reclamation, Bureau of Indian Affairs, and Non-Federal Water Management and Maintenance Activities on the Middle Rio Grande, New Mexico Middle Rio Grande Project, New Mexico San Juan-Chama Project, New Mexico Upper Colorado Region U.S. Department of the Interior Bureau of Reclamation August 2015 Mission Statements The U.S. Department of the Interior protects America’s natural resources and heritage, honors our cultures and tribal communities, and supplies the energy to power our future. The mission of the Bureau of Reclamation is to manage, develop, and protect water and related resources in an environmentally and economically sound manner in the interest of the American public. The Bureau of Indian Affairs’ mission is to enhance the quality of life, to promote economic opportunity, and to carry out the responsibility to protect and improve the trust assets of American Indians, Indian tribes and Alaska Natives. U.S. Department of the Interior Bureau of Reclamation August 2015 Joint Biological Assessment Bureau of Reclamation, Bureau of Indian Affairs, and Non- Federal Water Management and Maintenance Activities on the Middle Rio Grande, New Mexico Part I – Action Area and Species-Related Information Middle Rio Grande Project, New Mexico San Juan-Chama Project, New Mexico Upper Colorado Region Submitted to the U.S. Fish and Wildlife Service Rio Grande Silvery Minnow Southwestern Willow Flycatcher Yellow-billed Cuckoo New Mexico Meadow Jumping Mouse Pecos Sunflower Interior Least Tern U.S. Department of the Interior Bureau of Reclamation August 2015 Joint Biological Assessment Part I – Action Area and Species-Related Information Table of Contents 1. Introduction ............................................................................................................................ I-1 1.1 Biological Assessment Content and Scope .................................................................... I-1 1.1.1 Scope of Consultation Compared to 2003 BO ...................................................... I-1 1.1.2 Scope of Consultation Related to San Juan Chama Project .................................. I-3 1.2 Overview of Project Components .................................................................................. I-3 1.2.1 The San Juan-Chama Project ................................................................................ I-3 1.2.1.1 Heron Dam and Reservoir ...................................................................... I-4 1.2.1.2 Nondiscretionary Duties and the Minnow Rider .................................... I-4 1.2.2 The Middle Rio Grande Project, Including the MRGCD ..................................... I-5 1.2.2.1 The History of the MRG Project ............................................................ I-5 1.2.2.2 El Vado Dam and Reservoir ................................................................... I-7 1.2.2.3 The MRGCD Divisions .......................................................................... I-8 1.2.2.3.1 Cochiti Division ..................................................................... I-8 1.2.2.3.2 Albuquerque Division ............................................................ I-8 1.2.2.3.3 Belen Division ....................................................................... I-9 1.2.2.3.4 Socorro Division .................................................................... I-9 1.2.2.4 The MRG Project Diversion Dams ........................................................ I-9 1.2.2.5 The MRG Project and MRGCD Water Rights ..................................... I-10 1.2.2.6 The Low Flow Conveyance Channel ................................................... I-11 1.2.3 Responsibilities and Actions of the State of New Mexico ................................. I-11 1.2.3.1 Administration of the Rio Grande Compact ......................................... I-11 1.2.3.2 Administration of Surface Water and Groundwater Supplies .............. I-11 1.2.3.3 Administration of Domestic, Municipal, Livestock, and Temporary Uses .................................................................................... I-12 1.3 Overview of Water Operations ..................................................................................... I-12 1.3.1 The Rio Grande Compact and Article VII Storage Restrictions ......................... I-13 1.3.2 Water Accounting ............................................................................................... I-14 1.3.3 Snowmelt Forecasting and the Upper Rio Grande Water Operations Model ..................................................................................... I-14 1.3.4 The Annual Operating Plan ................................................................................ I-15 1.3.5 Prior and Paramount Operations ......................................................................... I-16 1.3.6 MRGCD Water Management ............................................................................. I-17 1.3.6.1 MRGCD Borrow/Payback Arrangements ............................................ I-17 1.3.6.2 MRGCD Measurement ......................................................................... I-18 1.4 Overview of River and Infrastructure Maintenance and Restoration ........................... I-18 1.5 Projects Not Included in the Biological Assessment .................................................... I-19 1.6 Reclamation’s Tribal Trust Responsibility and ESA Compliance .............................. I-20 I-i Joint Biological Assessment Part I – Action Area and Species-Related Information Table of Contents (cont.) 1.6.1 Indian Water Rights Settlements ........................................................................ I-21 1.7 The Middle Rio Grande Endangered Species Collaborative Program ......................... I-22 1.8 Consultation and Litigation History ............................................................................. I-24 1.8.1 Early Coordination Efforts .................................................................................. I-26 1.9 Quiet Title Litigation History ....................................................................................... I-28 2. Action Area .......................................................................................................................... I-30 2.1 Reclamation and BIA ................................................................................................... I-30 2.1.1 Water Operations ................................................................................................ I-32 2.1.2 River Maintenance .............................................................................................. I-32 2.1.2.1 Middle Rio Grande ............................................................................... I-32 2.1.2.2 Delta Channel ....................................................................................... I-33 2.2 Other Reclamation MRG Activities ............................................................................. I-33 2.3 State of New Mexico .................................................................................................... I-33 2.4 Middle Rio Grande Conservancy District .................................................................... I-34 3. Species Description, Federal Listing Status, and Life History ............................................ I-35 3.1 Rio Grande Silvery Minnow ........................................................................................ I-35 3.1.1 Species Description ............................................................................................. I-35 3.1.2 Distribution and Abundance ............................................................................... I-35 3.1.2.1 Population Monitoring .......................................................................... I-36 3.1.2.2 Population Estimation .......................................................................... I-37 3.1.2.3 Spawning Monitoring and Entrainment ............................................... I-37 3.1.2.4 Status of Silvery Minnow in the MRG ................................................. I-37 3.1.2.4.1 Spawning ............................................................................. I-37 3.1.2.4.2 Population Dynamics ........................................................... I-40 3.1.2.4.3 Genetic Monitoring .............................................................. I-44 3.1.2.4.4 Water Quality and Fish Health Monitoring ......................... I-47 3.1.3 Listing Status – Critical Habitat .......................................................................... I-49 3.1.4 Life History and Ecology .................................................................................... I-50 3.1.5 Reasons for Decline ............................................................................................ I-54 3.2 Southwestern Willow Flycatcher ................................................................................. I-56 3.2.1 Species Description ............................................................................................. I-56 3.2.2 Distribution and Abundance ............................................................................... I-58 3.2.3 Listing Status and Critical Habitat ...................................................................... I-63 3.2.4 Life History and Ecology .................................................................................... I-66 3.2.4.1