PROGRAMMATIC BIOLOGICAL ASSESSMENT OF BUREAU OF RECLAMATION’S WATER AND RIVER MAINTENANCE OPERATIONS, ARMY CORPS OF ENGINEERS’ FLOOD CONTROL OPERATION, AND NON-FEDERAL ACTIONS ON THE MIDDLE RIO GRANDE, NEW MEXICO March 1, 2003 – February 28, 2013 Partially incorporating the 2001 Biological Assessment Submitted to the U. S. Fish and Wildlife Service RIO GRANDE SILVERY MINNOW SOUTHWESTERN WILLOW FLYCATCHER BALD EAGLE INTERIOR LEAST TERN February 19, 2003 U. S. Department of the Interior U. S. Army Corps of Engineers Bureau of Reclamation Albuquerque District Albuquerque Area Office Albuquerque, New Mexico Albuquerque, New Mexico TABLE OF CONTENTS 1 INTRODUCTION.................................................................................................................................................1 1.1 Biological Assessment Content and Scope................................................................................1 1.2 Summary of Recent Consultation Activities..............................................................................1 1.3 Summary of Minnow v. Keys Litigation and 2003 Consultation Approach..............................1 2 AREA OF ACTION ..............................................................................................................................................3 3 DESCRIPTION OF PROPOSED ACTIONS........................................................................................................5 3.1 Introduction................................................................................................................................5 3.2 Non-Federal Actions..................................................................................................................5 3.2.1.1 State of New Mexico .................................................................................................................6 3.2.1.2 Counties .....................................................................................................................................6 3.2.1.3 Villages, Towns, and Cities .......................................................................................................6 3.2.1.4 Irrigation Interests......................................................................................................................6 3.3 Federal Actions..........................................................................................................................7 3.3.1 Corps of Engineers.....................................................................................................................7 3.3.2 Bureau of Reclamation ..............................................................................................................8 3.3.2.1 Closed Basin Division, San Luis Valley Project........................................................................8 3.3.2.2 San Juan-Chama Project ............................................................................................................8 3.3.2.3 Middle Rio Grande Project ......................................................................................................10 3.3.2.4 Annual Operating Plan.............................................................................................................12 3.3.2.5 Adaptive Management and Monitoring ...................................................................................13 4 SPECIES STATUS AND LIFE HISTORY ........................................................................................................14 4.1 Rio Grande Silvery Minnow....................................................................................................14 4.1.1 Status and Distribution.............................................................................................................14 4.1.2 Life History and Ecology.........................................................................................................14 4.1.3 Reasons for Decline .................................................................................................................16 4.2 Southwestern Willow Flycatcher.............................................................................................18 4.2.1 Status and Distribution.............................................................................................................18 4.2.2 Life History and Ecology.........................................................................................................20 4.2.3 Reasons for Decline .................................................................................................................21 4.3 Bald Eagle................................................................................................................................22 4.3.1 Status and Distribution.............................................................................................................22 4.3.2 Life History and Ecology.........................................................................................................25 4.3.3 Reasons for Decline .................................................................................................................25 4.4 Interior Least Tern ...................................................................................................................25 4.4.1 Status and Distribution.............................................................................................................25 4.4.2 Life History and Ecology.........................................................................................................25 4.4.3 Reasons for Decline .................................................................................................................25 5 ENVIRONMENTAL BASELINE ......................................................................................................................26 5.1 Introduction..............................................................................................................................26 5.2 Corps of Engineers...................................................................................................................26 5.3 Proposed Federal Actions with Early or Completed Consultation...........................................26 5.3.1 Rio Grande and Low Flow Conveyance Channel Modifications.............................................26 5.3.2 Low Flow Conveyance Channel Experimental Operations .....................................................26 5.3.3 Low Flow Conveyance Channel Mowing................................................................................27 5.3.4 Elephant Butte Temporary Channel Project ............................................................................27 5.3.5 Los Lunas Habitat Restoration Project ....................................................................................27 5.3.6 City of Albuquerque Drinking Water Project ..........................................................................28 5.3.7 Elephant Butte and Caballo Reservoirs Resource Management Plan EIS ...............................28 5.3.8 General Environmental Commitments from Early or Completed Consultations.....................28 5.3.8.1 Southwestern Willow Flycatcher.............................................................................................28 5.3.8.2 Rio Grande Silvery Minnow....................................................................................................29 5.3.8.3 Bald Eagle and Interior Least Tern..........................................................................................29 5.4 Contemporary Non-Federal Actions........................................................................................29 5.5 Geomorphology .......................................................................................................................29 5.6 Hydrology................................................................................................................................30 5.6.1 Article VII of the Rio Grande Compact - Historic Duration of Storage Restrictions ..............31 5.6.2 Recent Water Operations .........................................................................................................31 5.6.3 Environmental Baseline Hydrology.........................................................................................34 5.7 Biology ....................................................................................................................................38 ii 5.7.1 Ichthyofauna ............................................................................................................................38 5.7.1.1 Regional, Community-based Perspectives of Diversity and Faunal Change ...........................38 5.7.1.1.1 Species Diversity as a Predictive Function of Watershed Area ...............................................39 5.7.1.1.2 Species Diversity as a Predictive Function of Phylogeny........................................................40 5.7.1.1.3 Species Diversity as a Predictive Function of Reproductive Guilds........................................42 5.7.1.2 Site-specific, Community-based Perspective of Diversity and Faunal Change .......................43 5.7.1.2.1 Index of Diversity ....................................................................................................................43 5.7.1.3 Population Level Perspectives .................................................................................................44