or UNITED STATES DEPARTMENT OF COMMERCE / National Oceanic and Atmospheric Administration * i. I NATIONAL MARINE FISHERIES SERVICE Southeast Regional Office 4rES O LQi 3U Ie1U SOU St. Petersburg, Florida 33701-5505 http://sero.nmfs.noaa.gov F/SER3 1: NMB SER-2015- 17616 NOV20 2017 Mr. Donald W. Kinard Chief, Regulatory Division U.S. Army Corps of Engineers P.O. Box 4970 Jacksonville, Florida 32232-0019 Ref.: U.S. Army Corps of Engineers Jacksonville District’s Programmatic Biological Opinion (JAXBO) Dear Mr. Kinard: Enclosed is the National Marine Fisheries Service’s (NMFS’s) Programmatic Biological Opinion (Opinion) based on our review of the impacts associated with the U.S. Army Corps of Engineers (USACE’s) Jacksonville District’s authorization of 10 categories of minor in-water activities within Florida and the U.S. Caribbean (Puerto Rico and the U.S. Virgin Islands). The Opinion analyzes the effects from 10 categories of minor in-water activities occurring in Florida and the U.S. Caribbean on sea turtles (loggerhead, leatherback, Kemp’s ridley, hawksbill, and green); smalitooth sawfish; Nassau grouper; scalloped hammerhead shark, Johnson’s seagrass; sturgeon (Gulf, shortnose, and Atlantic); corals (elkhom, staghorn, boulder star, mountainous star, lobed star, rough cactus, and pillar); whales (North Atlantic right whale, sei, blue, fin, and sperm); and designated critical habitat for Johnson’s seagrass; smalltooth sawfish; sturgeon (Gulf and Atlantic); sea turtles (green, hawksbill, leatherback, loggerhead); North Atlantic right whale; and elkhorn and staghorn corals in accordance with Section 7 of the Endangered Species Act. We also analyzed effects on the proposed Bryde’s whale. We based our analysis on project-specific information provided by USACE, consultants, and NMFS’s review of published literature. The Opinion concludes that the suite of activities evaluated within the Opinion is likely to adversely affect, but is not likely to jeopardize, the continued existence of Johnson’s seagrass and is likely to adversely affect, but is not likely to destroy or adversely modify, critical habitat for smalltooth sawfish and Johnson’s seagrass. We look forward to further cooperation with you on other USACE projects to ensure the conservation and recovery of our threatened and endangered marine species. If you have any questions regarding this consultation, please contact Nicole Bonine, Consultation Biologist, at (727) 824-5336, or by email at Nicole.Boninenoaa.gov. Sincerely, oy E. Crabtree, Ph.D. Regional Administrator Enclosure File: 1514-22.F.4 2 ____________________________ Endangered Species Act - Section 7 Consultation Biological Opinion Agency: United States Army Corps of Engineers, Jacksonville District Applicant: United States Army Corps of Engineers, Jacksonville District Activity: Authorization of Minor In-Water Activities throughout the Geographic Area of Jurisdiction of the U.S. Army Corps of Engineers Jacksonville District, including Florida and the U.S. Caribbean Consulting Agency: National Marine Fisheries Service Southeast Regional Office Protected Resources Division (SER-2015-17616) Date Issued: Approved By: Roy . Crabtree, Ph.D. Re onal Administrator 3 Table of Contents 1 Consultation History ......................................................................................................... 18 2 Description of the Proposed Action and Potential Routes of Effect to Species and Critical Habitat ............................................................................................................................... 20 2.1 Project Action Area ........................................................................................................ 23 2.1.1 Species Specific Restriction and Exclusion Zones within the Action Area ........... 24 2.1.2 USACE Effect Determinations for Listed Species and Critical Habitat................. 35 2.1.3 Listed Species and Critical Habitat Occurring within the Action Area .................. 38 2.2 Activities Analyzed, Project Design Criteria, and Potential Routes of Effect ............... 44 2.2.1 Activity 1 (A1): Shoreline Stabilization ................................................................. 96 2.2.2 Activity 2 (A2): Pile-Supported Structures and Anchored Buoys ........................ 109 2.2.3 Activity 3 (A3): Maintenance, Minor, and Muck Dredging ................................. 134 2.2.4 Activity 4 (A4): Water-Management Outfall Structures and Associated Endwalls .............................................................................................................................. 152 2.2.5 Activity 5 (A5): Scientific Survey Devices .......................................................... 164 2.2.6 Activity 6 (A6): Boat Ramps ................................................................................ 171 2.2.7 Activity 7 (A7): Aquatic Habitat Enhancement, Establishment, and Restoration Activities .............................................................................................................. 181 2.2.8 Activity 8 (A8): Transmission and Utility Lines .................................................. 203 2.2.9 Activity 9 (A9): Marine Debris Removal ............................................................. 216 2.2.10 Activity 10 (A10): Temporary Platforms, Fill, and Cofferdams .......................... 220 2.2.11 Summary and Cumulative Effect of Proposed Action to Listed Species and Critical Habitat .................................................................................................................. 233 2.3 Project-Specific Review ............................................................................................... 236 2.4 Programmatic Review .................................................................................................. 240 3 Status of Listed Species and Critical Habitat Likely to be Adversely Affected ............. 242 3.1 Status of Species Likely to be Adversely Affected ...................................................... 242 3.1.1 Johnson’s Seagrass................................................................................................ 242 3.2 Status of Critical Habitat Likely to be Adversely Affected ......................................... 252 3.2.1 Johnson’s Seagrass Critical Habitat ...................................................................... 252 3.2.2 Smalltooth Sawfish Critical Habitat ..................................................................... 255 4 Environmental Baseline .................................................................................................. 265 4.1 Factors Affecting Johnson’s Seagrass and Johnson’s Seagrass Critical Habitat in the Action Area .................................................................................................................. 265 4.1.1 Federal and State Actions ..................................................................................... 265 4 4.1.2 Conservation and Recovery Activities That May Benefit Johnson’s Seagrass and Johnson’s Seagrass Critical Habitat ..................................................................... 267 4.2 Factors Affecting Smalltooth Sawfish Critical Habitat within the Action Area .......... 267 4.2.1 Federal Actions ..................................................................................................... 267 4.2.2 State or Private Actions ........................................................................................ 267 4.2.3 Other Potential Factors ......................................................................................... 268 5 Effects of the Action ....................................................................................................... 268 5.1 Effects to Johnson’s Seagrass ...................................................................................... 268 5.2 Effects to Johnson’s Seagrass Critical Habitat ............................................................. 269 5.3 Effects to Smalltooth Sawfish Critical Habitat ............................................................ 270 6 Cumulative Effects.......................................................................................................... 271 6.1 Cumulative Effects to Johnson’s Seagrass and Johnson’s Seagrass Critical Habitat .. 271 6.2 Cumulative Effects to Smalltooth Sawfish Critical Habitat......................................... 272 7 Jeopardy Analysis ........................................................................................................... 273 7.1 Johnson’s Seagrass ....................................................................................................... 273 8 Destruction and Adverse Modification Analysis ............................................................ 275 8.1 Johnson’s Seagrass Critical Habitat ............................................................................. 276 8.2 Smalltooth Sawfish Critical Habitat ............................................................................. 277 8.2.1 Protect and Restore Smalltooth Sawfish Habitat (Recovery Objective #2) ......... 278 Shallow, Euryhaline Essential Feature Impacts ............................................................. 279 Red Mangrove Essential Feature Impacts ...................................................................... 281 Summary of Impacts to the Essential Features ............................................................... 283 8.2.2 Ensure Smalltooth Sawfish Abundance