University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln US Army Corps of Engineers U.S. Department of Defense 2006 BIOLOGICAL OPINION ON THE OPERATION OF THE MISSOURI RIVER MAIN STEM SYSTEM, MISSOURI RIVER BANK STABILIZATION AND NAVIGATION PROJECT, AND OPERATION OF THE KANSAS RIVER RESERVOIR SYSTEM Follow this and additional works at: https://digitalcommons.unl.edu/usarmyceomaha Part of the Civil and Environmental Engineering Commons "BIOLOGICAL OPINION ON THE OPERATION OF THE MISSOURI RIVER MAIN STEM SYSTEM, MISSOURI RIVER BANK STABILIZATION AND NAVIGATION PROJECT, AND OPERATION OF THE KANSAS RIVER RESERVOIR SYSTEM" (2006). US Army Corps of Engineers. 6. https://digitalcommons.unl.edu/usarmyceomaha/6 This Article is brought to you for free and open access by the U.S. Department of Defense at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in US Army Corps of Engineers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. 2006 ANNUAL REPORT BIOLOGICAL OPINION ON THE OPERATION OF THE MISSOURI RIVER MAIN STEM SYSTEM, MISSOURI RIVER BANK STABILIZATION AND NAVIGATION PROJECT, AND OPERATION OF THE KANSAS RIVER RESERVOIR SYSTEM February 22, 2007 Prepared By: U.S. Army Corps of Engineers Omaha District Kansas City District 2006 Annual Report Biological Opinion on the Operation of the Missouri River Main Stem System, Operation and Maintenance of the Missouri River Bank Stabilization and Navigation Project, and Operation of the Kansas River Reservoir System Table of Contents Introduction.....................................................................................................................................................1 I. Pallid Sturgeon (Scaphirhynchus albus)..................................................................................................1 II. Least Tern & Piping Plover (Sterna antillarum & Charadrius melodus)..........................................1 III. Ecosystem.................................................................................................................................................1 IV. Missouri River Comprehensive Recovery Program............................................................................1 I. Pallid Sturgeon...........................................................................................................................................1 I.A. Shallow Water Habitat Design and Construction Activities....................................................................1 I.A.1. Omaha District.......................................................................................................................................1 I.A.2. Kansas City District...............................................................................................................................3 I.B. Pallid Sturgeon Propagation/Augmentation Support................................................................................7 I.B.1. Bozeman Fish Technology Center (Bozeman FTC).............................................................................8 I.B.2. Miles City State Fish Hatchery (Miles City).........................................................................................9 I.B.3. Garrison Dam National Fish Hatchery (Garrison) ..............................................................................10 I.B.4. Gavins Point National Fish Hatchery (Gavins)...................................................................................11 I.B.6. Blind Pony State Fish Hatchery (Blind Pony).....................................................................................12 I.B.7. Neosho National Fish Hatchery (Neosho)...........................................................................................12 I.C. Pallid Sturgeon Population Assessment Implementation.......................................................................14 I.D. Research, Monitoring and Evaluation Activities....................................................................................16 I.D.1. Comprehensive Sturgeon Research Program......................................................................................16 I.D.2. Spring Rise Flow Modification...........................................................................................................16 I.D.3. Fort Peck Tests Biological Monitoring...............................................................................................17 I.D.4. Physical and Biological Monitoring-Shallow Water Habitat..............................................................19 II. Least Tern and Piping Plover................................................................................................................20 II.A. Preparation of a Programmatic Environmental Impact Statement for Emergent Sandbar Habitat (ESH) Creation Activities..................................................................................................20 II.B. Emergent Sandbar Habitat Creation Activities.....................................................................................21 II.C. Research, Monitoring, and Evaluation..................................................................................................22 II.C.1 Least Tern Summary...........................................................................................................................23 RPM 1 – Survey and Monitor Least Terns, Mortality and Incidental Take...................................................24 RPM 1.1 – Annual Least Tern Monitoring Program......................................................................................24 RPM 1.2 – Mortality of Adults, Chicks, Eggs and Nests...............................................................................29 RPM 4 – Monitor, Evaluate, and Modify Created and Rehabilitated Sandbars.............................................33 RPM 5 – Evaluate Effective Measures to Reduce Least Tern Predation.......................................................42 RPM 6 – Reduce Human Disturbance of Least Terns and Conduct Outreach and Education.......................42 RPM 7 – Revise Contingency Plan for Moving Eggs....................................................................................44 i II.C.2. Piping Plover Summary......................................................................................................................44 1. Take (killing) of eggs and chicks by flooding on the river and reservoir reaches that results from the Corps’ operation of the water control system................................................................................45 2. Take (harm) of eggs, chick, or adults by predation...................................................................................48 3. Take (harm) of eggs, chicks, or adults by human disturbance..................................................................48 4. Take (harm) of chicks as a result of insufficient forage in river reaches affected by hypolimnetic releases..............................................................................................................................48 5. Take (harm) of eggs in nests assigned fates of destroyed-unknown, nest abandonment, sandbar erosion, and unknown fates.............................................................................................................49 6. Take (harm) of chicks as a result of insufficient forage on created habitats.............................................49 RPM 1.1 Annual Piping Plover Monitoring Program...................................................................................50 RPM 1.2 – Survival Information....................................................................................................................54 RPM 1.3 Nests and Eggs Loss........................................................................................................................56 RPM 2.2 Adult and Chick Mortality..............................................................................................................57 RPM 3 – The Corps shall coordinate regularly with the U.S. Fish & Wildlife Service to ensure that operations minimize take...........................................................................................................58 RPM 4 – The Corps shall collaborate with the Service … to develop criteria and procedures for the moving of eggs and chicks................................................................................................................58 RPM 5 – The Corps shall implement public information and education programs to increase public awareness to reduce take of nesting piping plovers............................................................59 RPM 5.2 Public Relations...............................................................................................................................59 RPM 5.3 Posting of Piping Plover Nesting Areas..........................................................................................59 RPM 6- The Corps shall evaluate and implement actions to reduce predation on piping plover nests, chicks and adults......................................................................................................................59 RPM 8 – The Corps shall develop and implement a program to monitor and evaluate the effectiveness of created sandbars as nesting habitat for piping plovers.................................................61 II.D. 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