REVISED DRAFT - 8/21/00 BIOLOGICAL OPINION ON THE OPERATION OF THE MISSOURI RIVER MAIN STEM RESERVOIR SYSTEM,
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1 REVISED DRAFT - 8/21/00 BIOLOGICAL OPINION ON THE OPERATION OF THE MISSOURI RIVER MAIN STEM RESERVOIR SYSTEM, OPERATION AND MAINTENANCE OF THE MISSOURI RIVER BANK STABILIZATION AND NAVIGATION PROJECT, AND OPERATION OF THE KANSAS RIVER RESERVOIR SYSTEM (JULY 2000) Prepared by: U.S. Fish and Wildlife Service Region 6, Denver, Colorado Region 3, Fort Snelling, Minnesota
2 TABLE OF CONTENTS Page LIST OF FIGURES... LIST OF TABLES... LIST OF ACRONYMS... LIST OF SCIENTIFIC NAMES... INTRODUCTION... SPECIES COVERED IN THIS CONSULTATION... CONSULTATION HISTORY... OPERATION OF THE MISSOURI RIVER MAIN STEM RESERVOIR SYSTEM... OPERATION OF THE KANSAS RIVER RESERVOIR SYSTEM... OPERATION AND MAINTENANCE OF THE MISSOURI RIVER BANK STABILIZATION AND NAVIGATION PROJECT... HISTORY FOR COMBINED CONSULTATION ON MISSOURI RIVER PROJECTS (MR PROJECTS) BIOLOGICAL OPINION... DESCRIPTION OF THE PROPOSED ACTION... ACTION AREA... OPERATION OF THE MISSOURI RIVER MAIN STEM RESERVOIR SYSTEM... Generic Description of Project and Authorizing Legislation... Master Manual... Current Water Control Plan... Annual Operating Plan... Flood Control... Irrigation... Municipal, Industrial, and Rural Water Supply... Navigation... -ii-
3 Power Production... Water Quality... Recreation... Fish and Wildlife... Intra-System Regulation... Short-Term and Long-Term Adjustments... System Limitations... System Flexibility... Synthetic Models for System Regulation... Conservation Measures for Threatened and Endangered Species... OPERATION OF THE KANSAS RIVER RESERVOIR SYSTEM... Generic Description of Project and Authorizing Legislation... Operations of Tributary Lakes and Local Protection Projects... Flood Control Municipal, Industrial, and Rural Water Supply and Water Quality Irrigation... Navigation... Hydropower... Recreation... Fish and Wildlife... System Limitations... System Flexibility... Conservation Measures for Threatened and Endangered Species... OPERATION AND MAINTENANCE OF THE MISSOURI RIVER BANK STABILIZATION AND NAVIGATION PROJECT... Generic Description of Project and Authorizing Legislation... Operation and Maintenance... Changes to Established Operation & Maintenance Practices... History of Modification for Fish and Wildlife Habitat Improvement... Conservation Measures for Threatened and Endangered Species... STATUS OF LISTED SPECIES RANGE WIDE... BALD EAGLE... Species Description... Historic and Current Range Wide Distribution... Life History... Reproductive Biology... Age and Growth... Movements... Population Status and Trends... Habitat and Food Requirements... Habitat Characteristics... -iii-
4 Food and Feeding Habits... Range Wide Distribution and Abundance of Habitat... Factors Affecting the Species Range Wide... Habitat Loss and Degradation... Pollution/Contaminants... Summary... LEAST TERN... Species Description... Historic and Current Range Wide Distribution... Life History... Reproductive Biology... Growth and Longevity... Movements/Dispersal Patterns... Population Status and Trends... Habitat and Food Requirements... Habitat Characteristics... Food and Feeding Habits... Range Wide Distribution and Abundance of Habitat... Factors Affecting the Species Range Wide... Habitat Loss and Degradation... Human Disturbance... Pollution/Contaminants... Summary... PIPING PLOVER... Species Description... Historic and Current Range Wide Distribution... Life History... Reproductive Biology... Growth and Longevity... Movements/Dispersal Patterns... Population Status and Trends... Habitat and Food Requirements... Habitat Characteristics... Food and Feeding Habits... Range Wide Distribution and Abundance of Habitat... Factors Affecting the Species Range Wide... Habitat Loss and Degradation... Human Disturbance... Pollution/Contaminants... Summary... PALLID STURGEON... Species Description... -iv-
5 Genetics... Historic and Current Range Wide Distribution... Life History... Reproductive Biology... Age and Growth... Movements... Population Status and Trends... Habitat and Food Requirements... Habitat Characteristics... Micro-Habitat Characteristics... Food and Feeding Habits... Range Wide Distribution and Abundance of Habitat... Factors Affecting the Species Range Wide... Habitat Loss and Degradation... Commercial Harvest... Pollution/Contaminants... Hybridization... Summary... ENVIRONMENTAL BASELINE WITHIN THE ACTION AREA... STATUS OF THE SPECIES WITHIN THE ACTION AREA AND THE ECOSYSTEMS UPON WHICH THEY DEPEND... MISSOURI RIVER SYSTEM... Historical Perspective... Description of Existing Missouri River System... Importance of the Missouri River Ecosystem... KANSAS RIVER SYSTEM... Historical Perspective... Description of Existing Kansas River System... Importance of the Kansas River Ecosystem... MISSOURI AND KANSAS RIVER SECTIONS AND SEGMENTS... BALD EAGLE... Historic and Current Distribution in the Action Area... Population Status and Trends in the Action Area... Distribution and Abundance of Habitat in the Action Area... Productivity and Recovery Objective in the Action Area... Importance of the Missouri River to the Bald Eagle... Importance of the Kansas River to the Bald Eagle... LEAST TERN... -v-
6 Historic and Current Distribution in the Action Area... Population Status and Trends in the Action Area... Distribution and Abundance of Habitat in the Action Area... Productivity and Recovery Objective in the Action Area... Importance of the Missouri River to the Least Tern... Importance of the Kansas River to the Least Tern... PIPING PLOVER... Historic and Current Distribution in the Action Area... Population Status and Trends in the Action Area... Distribution and Abundance of Habitat in the Action Area... Productivity and Recovery Objective in the Action Area... Importance of the Missouri River to the Piping Plover... Importance of the Kansas River to the Piping Plover... PALLID STURGEON... Historic and Current Distribution in the Action Area... Population Status and Trends in the Action Area... Distribution and Abundance of Habitat in the Action Area... Productivity and Recovery Objective in the Action Area... Importance of the Missouri River to the Pallid Sturgeon... Importance of the Kansas River to the Pallid Sturgeon... FACTORS AFFECTING THE SPECIES WITHIN THE ACTION AREA UNRELATED FEDERAL PROJECTS... Flood Initiatives... Emergency Wetland Reserve Program and Wetland Reserve Program... Federal Levee Projects... Federal Emergency Management Agency... Refuge Land Acquisition and Management... Sand and Gravel Dredging... Federal Highway Administration Bridge Projects... Corps of Engineers Section 1135 Projects... Recreational Rivers and National Wild and Scenic Rivers Act... Title VI Projects... State of South Dakota Recreation Sites Lease Proposal... Corps of Engineers Pierre/Fort Pierre Sedimentation Study... Corps of Engineers Pierre/Fort Pierre Relocation Effort... Section 32/33 Bank Stabilization Program... Section 404 Program... IMPACTS OF CONTEMPORANEOUS NON-FEDERAL ACTIONS... Tribal Water Rights and Natural Resource Management... Land Acquisition... -vi-
7 Floodplain Development... Recreational Development... Lewis and Clark Initiative... Commercial Fish Harvest... EFFECTS (DIRECT AND INDIRECT) OF THE FEDERAL ACTION... MISSOURI RIVER SYSTEM... BALD EAGLE... LEAST TERN AND PIPING PLOVER... PALLID STURGEON... KANSAS RIVER SYSTEM... BALD EAGLE... LEAST TERN AND PIPING PLOVER... PALLID STURGEON... INTERRELATED AND INTERDEPENDENT ACTIONS... Power Marketing... Missouri River Fish and Wildlife Mitigation Project... Water Depletion Projects... CUMULATIVE EFFECTS... CONCLUSION... BALD EAGLE... LEAST TERN... PIPING PLOVER... PALLID STURGEON... REASONABLE AND PRUDENT ALTERNATIVE... RPA MEASURES APPLICABLE TO MULTIPLE LISTED SPECIES IN THE ECOSYSTEM ADAPTIVE MANAGEMENT... Agency Coordination Team... Endangered Species and Habitat Monitoring Program... Annual Report... FLOW ENHANCEMENT... Gavins Point... Fort Peck... Other Segments... -vii-
8 UNBALANCED INTRASYSTEM REGULATION... HABITAT RESTORATION/CREATION/ACQUISITION... RPA MEASURES APPLICABLE TO SPECIFIC SPECIES... LEAST TERN AND PIPING PLOVER... PALLID STURGEON... INCIDENTAL TAKE STATEMENT... BALD EAGLE... AMOUNT OR EXTENT OF TAKE ANTICIPATED... EFFECT OF THE TAKE... REASONABLE AND PRUDENT MEASURES TO MINIMIZE TAKE... TERMS AND CONDITIONS FOR IMPLEMENTATION OF REASONABLE AND PRUDENT MEASURES... CLOSING... LEAST TERN AND PIPING PLOVER... AMOUNT OR EXTENT OF TAKE ANTICIPATED... EFFECT OF THE TAKE... REASONABLE AND PRUDENT MEASURES TO MINIMIZE TAKE... TERMS AND CONDITIONS FOR IMPLEMENTATION OF REASONABLE AND PRUDENT MEASURES... CLOSING... PALLID STURGEON... AMOUNT OR EXTENT OF TAKE ANTICIPATED... EFFECT OF THE TAKE... REASONABLE AND PRUDENT MEASURES TO MINIMIZE TAKE... -viii-
9 TERMS AND CONDITIONS FOR IMPLEMENTATION OF REASONABLE AND PRUDENT MEASURES... CLOSING... CONSERVATION RECOMMENDATIONS... RECOMMENDATIONS APPLICABLE TO MULTIPLE SPECIES... RECOVERY AND IMPLEMENTATION PROGRAM... BALD EAGLE... LEAST TERN AND PIPING PLOVER... PALLID STURGEON... SUMMARY TABLES... REINITIATION NOTICE... LITERATURE CITED... -ix-
10 APPENDIX I. COORDINATION WITH FEDERAL/STATE/TRIBAL GOVERNMENTS... II. III. ROUTINE ANNUAL MAINTENANCE SCHEDULES - BANK STABILIZATION AND NAVIGATION PROJECT AND 1988 MISSOURI RIVER CONDITIONS (DISCHARGE/DEPTH/HABITAT RELATIONSHIPS) AT SELECTED SITES (COLORED MAPS)... IV. SUMMARY OF PAST IMPACTS TO THE MISSOURI RIVER ECOSYSTEM... V. MISSOURI AND KANSAS RIVER SECTIONS AND SEGMENTS... VI. POPULATION DISTRIBUTION OF BREEDING AND WINTERING BALD EAGLES ON THE MISSOURI RIVER MAIN STEM... VII. SCIENTIFIC EVALUATION OF THE ROLE OF RIVER HYDROLOGY IN THE CONSERVATION OF MISSOURI RIVER ENDANGERED SPECIES VIII. CONTINGENCY PLAN FOR PROTECTION OF LEAST TERN AND PIPING PLOVER NESTS AND CHICKS -x-
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