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

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

Table of Contents

1 Consultation History 2 Description of the Proposed Action and Potential Routes of Effect to Species and Critical

Habitat

2.1 Project Action Area

2.1.1 Species Specific Restriction and Exclusion Zones within the Action Area

2.1.2 USACE Effect Determinations for Listed Species and Critical Habitat

2.1.3 Listed Species and Critical Habitat Occurring within the Action Area

2.2 Activities Analyzed, Project Design Criteria, and Potential Routes of Effect

2.2.1 Activity 1 (A1): Shoreline Stabilization

2.2.2 Activity 2 (A2): Pile-Supported Structures and Anchored Buoys

2.2.3 Activity 3 (A3): Maintenance, Minor, and Muck Dredging

2.2.4 Activity 4 (A4): Water-Management Outfall Structures and Associated Endwalls

2.2.5 Activity 5 (A5): Scientific Survey Devices

2.2.6 Activity 6 (A6): Boat Ramps

2.2.7 Activity 7 (A7): Aquatic Habitat Enhancement, Establishment, and Restoration

Activities

2.2.8 Activity 8 (A8): Transmission and Utility Lines

2.2.9 Activity 9 (A9): Marine Debris Removal

2.2.10 Activity 10 (A10): Temporary Platforms, Fill, and Cofferdams

2.2.11 Summary and Cumulative Effect of Proposed Action to Listed Species and Critical

Habitat

2.3 Project-Specific Review

2.4 Programmatic Review

3 Status of Listed Species and Critical Habitat Likely to be Adversely Affected

3.1 Status of Species Likely to be Adversely Affected

3.1.1 Johnson’s Seagrass

3.2 Status of Critical Habitat Likely to be Adversely Affected

3.2.1 Johnson’s Seagrass Critical Habitat

3.2.2 Smalltooth Sawfish Critical Habitat

4 Environmental Baseline

4.1 Factors Affecting Johnson’s Seagrass and Johnson’s Seagrass Critical Habitat in the

Action Area

4.1.1 Federal and State Actions

4.1.2 Conservation and Recovery Activities That May Benefit Johnson’s Seagrass and Johnson’s Seagrass Critical Habitat

4.2 Factors Affecting Smalltooth Sawfish Critical Habitat within the Action Area

4.2.1 Federal Actions

4.2.2 State or Private Actions

4.2.3 Other Potential Factors

5 Effects of the Action

5.1 Effects to Johnson’s Seagrass

5.2 Effects to Johnson’s Seagrass Critical Habitat

5.3 Effects to Smalltooth Sawfish Critical Habitat

6 Cumulative Effects

6.1 Cumulative Effects to Johnson’s Seagrass and Johnson’s Seagrass Critical Habitat .. 271

6.2 Cumulative Effects to Smalltooth Sawfish Critical Habitat

7 Jeopardy Analysis

7.1 Johnson’s Seagrass

8 Destruction and Adverse Modification Analysis

8.1 Johnson’s Seagrass Critical Habitat

8.2 Smalltooth Sawfish Critical Habitat

8.2.1 Protect and Restore Smalltooth Sawfish Habitat (Recovery Objective #2) Shallow, Euryhaline Essential Feature Impacts Red Mangrove Essential Feature Impacts Summary of Impacts to the Essential Features

8.2.2 Ensure Smalltooth Sawfish Abundance Increases (Recovery Objective #3)

9 Conclusion 10 Incidental Take Statement 11 Conservation Recommendations 12 Reinitiation of Consultation 13 Literature Cited 14 Appendix A: Authorities under which an Action Will Be Conducted

14.1.1 Current Permits Used to Authorize Projects in Florida under NMFS Jurisdiction

15 Appendix B: In-water Construction Noise

15.1 Glossary of Acoustic Terms

15.2 How in-water Noise effects ESA-listed Species Are Evaluated

15.2.1 Exposure Criteria Used to Determine Potential Effects

15.3 Calculations of Noise Thresholds for Pile Driving

15.3.1 Pile-Driving Noise Calculations

15.3.2 Noise Control Measures to Reduce Injury

15.3.3 Bubble Curtain Specifications for Pile Driving

15.4 How to Calculate Noise Impacts

15.4.1 Calculation Steps for Pile Driving

15.4.2 Example Noise Calculation for a Single Family Dock

16 Appendix C: North Atlantic Right Whale Information Form 17 Appendix D: Frac-Out Plan Example

List of Figures

Figure 1. Smalltooth sawfish limited exclusion zones

Figure 2. Gulf sturgeon critical habitat. Estuarine critical habitat units under NMFS’s jurisdiction shaded and the rivers under USFWS’s jurisdiction labeled (Images provided on the NMFS website at http://sero.nmfs.noaa.gov/maps_gis_data/protected_resources/critical_habitat/index.html)

Figure 3. Atlantic sturgeon critical habitat (Images provided on the NMFS website at http://sero.nmfs.noaa.gov/protected_resources/sturgeon/documents/critical_habitat_maps.pdf). 30

Figure 4. North Atlantic right whale educational sign zones

Figure 5. Sea turtle critical habitat in the U.S. Caribbean. NA DPS of green sea turtle critical habitat (left image), hawksbill sea turtle critical habitat (center image), and leatherback sea turtle critical habitat (right image)

Figure 6. Bryde’s whale exclusion zone

Figure 7. Number of registered vessels in Florida from 2005 to 2015 (Florida Department of Highway Safety and Motor Vehicle website: http://www.flhsmv.gov/dmv/vslfacts.html)

Figure 8. Example of a confined space (left) and an open-water environment (right) for a noise analysis

Figure 9. Example images of shoreline armoring and stabilization. The left image is a concrete slab seawall, the middle is a riprap shoreline, and the right is a vinyl seawall. (Images provided by the Florida Marine Contractors Association in 2014)

Figure 10. Examples of dock shapes, including T-shaped and L-shaped docks (©2014 Google).

Figure 11. Pile-supported Structures. Example of a marginal dock on the left, boatlift with I-beam in the middle, and a chickee on the right. (The left and middle photos were provided by the Florida Marine Contractors Association and right photo from www.cnn.com.)

Figure 12. Sample Marina Images. The left image shows an example of an open water marina (provided by the Florida Marine Contractors Association), while the right image shows an example of marina contained within an upland cut basin (©2014 Google)

Figure 13. Canal dredging footprint drawing

Figure 14. Mechanical dredge (clamshell bucket and barge)

Figure 15. Cutterhead pipeline dredge schematic and representative close-up photographs (provided by USACE)

Figure 16. Sample drawing of an outfall pipe with a manatee grate. Manatee grates are typically attached to the pipe, but in this case, piles are placed in front of the pipe

Figure 17. Example drawing of a boat ramp installed by placing prefabricated concrete slabs.

Note that excavation for this example was minimal (removed approximately 10 cubic yards in this instance) and limited to shaping the slope of the boat ramp. This ramp extends to -3 ft MLW. Drawings prepared by Glen Boe and Associates, Inc. submitted to NMFS as part of a consultation request

Figure 18. Oyster reefs. The left image shows oyster bags, the middle is an oyster mat, and the right is a barge filled with loose oyster cultch. All 3 images are from the Charlotte Harbor Habitat Restoration Plan (Boswell et al. 2012)

Figure 19. Living shoreline. This sample living shoreline cross-section is provided by NOAA’s Habitat Conservation and Restoration website (http://www.habitat.noaa.gov/restoration/techniques/lsimplementation.html)

Figure 20. Seagrass restoration. The left image is the placement of sediment to return a blowhole to pre-injury elevation. The image on the right shows bird stakes placed in a restoration area (Both images are from www.darrp.noaa.gov)

Figure 21. Artificial reef materials. The left image is an open top and bottom tetrahedron design, the middle image is a series of discs mounted to a pile, and the right image is a reef ball. Left and middle images are from Reef Maker (http://www.reefmaker.com) and the right image is from the Reef Ball Foundation (www.reefball.org)

Figure 22. Sample image of horizontal directional drilling (Image from Underground Solutions at http://www.undergroundsolutions.com)

Figure 23. Cathodic pile jacket (Image provided by USACE)

Figure 24. Structural cathodic pile jacket (Image provided by USACE)

Figure 25. Map of smalltooth sawfish critical habitat –CHEU and TTIEU

Figure 26. Diagram of a dredged channel

Figure 27. From left to right: current shoreline, + 3.5 in (+ 9 cm); + 18.5 in (+ 47 cm); and +

38.97 in (+ 99 cm) sea level rise by 2060

Figure 28. The relative effects to animals: distance to/from a noise source

Figure 29. Example of a confined space for a noise analysis. The left image shows a 150 ft radius in a channel resulting in the channel not being wide enough to ensure more than half the channel was free from cumulative injurious noise levels. The right image shows a portion of San Juan Harbor and a 260 ft radius that would not block movement of species if piles were installed at this location because species would be able to move along the left side of the image between the 2 structures

Figure 30. An example of intermediate spreading loss where surface reflections result in non-uniform spreading of sound waves

Figure 31. Screenshot of the Spreading Loss Calculator. The dB loss over any range can be determined for 3 types spreading loss models (10 logR, 15 logR, and 20 logR). For example, at 50 m, there is a 25.5 dB reduction in noise from a pile due to intermediate transmission loss (15 logR)

Figure 32. An example graphic visualizing impact zones for a pile-driving project. Graphical representations of the impact zones are useful analytical tools in visualizing the area where project impacts will occur within the species’ habitat

Figure 33. Screenshot of original Spreading Loss Calculator prior to any modifications

Figure 34. Screenshot of the Spreading Loss Calculator after the first column was modified .. 331

List of Tables

Table 1. Limited Exclusion Zones in Smalltooth Sawfish Critical Habitat

Table 2. Gulf sturgeon critical habitat migratory restriction zones

Table 3. North Atlantic Right Whale Educational Sign Zone

Table 4. USACE Project Effects Determinations for Activities Occurring in Florida

Table 5. Listed Species NMFS Believes Are Likely to Occur in or near the Action Area

Table 6. Designated Critical Habitat NMFS Believes is In or Near the Action Area

Table 7. Essential Features/PCEs/PBFs of Each Critical Habitat Unit in Florida and the U.S.

Caribbean

Table 8. Projected Number of Authorizations Occurring in Certain Critical Habitat Units per Activity for 5-year Period

Table 9. NMFS Effects Determinations for Johnson’s Seagrass

Table 10. NMFS Effects Determinations for Nassau Grouper

Table 11. NMFS Effects Determinations for the Central and Southwest Atlantic DPS of Scalloped Hammerhead Shark

Table 12. NMFS Effects Determinations for ESA-listed Whales

Table 13. NMFS Effects Determinations for NWA DPS of Loggerhead Sea Turtle Critical Habitat

Table 14. NMFS Effects Determinations for Acropora Critical Habitat

Table 15. NMFS Effects Determination for North Atlantic Right Whale Critical Habitat

Table 16. NMFS Effects Determination for Green, Hawksbill, and Leatherback Sea Turtle Critical Habitat

Table 17. NMFS Effects Determination for Atlantic Sturgeon Critical Habitat

Table 18. Impact Hammer Sound Source Levels and Impact Radius Distances

Table 19. Vibratory Hammer Sound Source Levels and Impact Radius Distances

Table 20. NMFS Effects Determinations for In-water Construction Noise Analyzed under this Opinion to Sea Turtles and ESA-listed Fish

Table 21. USACE and NMFS Determinations on the Effects of Shoreline Stabilization Activities (Activity 1) to ESA-listed Species listed in Table 5

Table 22. Estimated Amount of Waterbottom Affected By Shoreline Stabilization Projects per 5-Year Period

Table 23. USACE and NMFS Determinations on the Effects of Shoreline Stabilization Activities (Activity 1) to Designated Critical Habitat

Table 24. Estimated Amount of Waterbottom Affected By Shoreline Stabilization Projects in Smalltooth Sawfish, Gulf Sturgeon, and Johnson’s Seagrass Critical Habitat per 5-Year Period

Table 25. USACE and NMFS Determinations on the Effects of Pile-Supported Structures and Anchored Buoys (Activity 2) to ESA-listed Species listed in Table 5

Table 26. Estimated Amount of Waterbottom Affected by Pile-Supported Structures and Anchored Buoys Occurring Outside of Johnson’s Seagrass Critical per 5-Year Period

Table 27. Estimated Amount of Waterbottom Affected by Pile-Supported Structures and Anchored Buoys Occurring Within Johnson’s Seagrass Critical Habitat per 5-Year Period

Table 28. USACE and NMFS Determinations on the Effects of Pile-Supported Structures and Anchored Buoys (Activity2) to Designated Critical Habitats

Table 29. Estimated Amount of Waterbottom Affected by Pile-Supported Structures and Anchored Buoys Occurring Within Smalltooth Sawfish Critical Habitat per 5-Year Period

Table 30. Estimated Amount of Waterbottom Affected by Pile-Supported Structures and Anchored Buoys Occurring Within Gulf Sturgeon Critical Habitat per 5-Year Period

Table 31. USACE and NMFS Determinations on the Effects of Dredging Activities (Activity 3) to ESA-listed Species listed in Table 5

Table 32. Estimated Amount of Waterbottom Affected by Dredging Activities Per 5-Year Period

Table 33. USACE and NMFS Determinations on the Effect of Dredging Activities (Activity 3) on Designated Critical Habitat

Table 34. Total Waterbottom Affected by Dredging Projects within Smalltooth Sawfish, Gulf Sturgeon, and Johnson’s Seagrass Critical Habitat

Table 35. USACE and NMFS Determinations on the Effects of Water-Management Outfall Structures and Associated Endwall Activities (Activity 4) to ESA-listed Species Listed in Table

Table 36. Estimated Amount of Waterbottom and Shoreline Areas and Mangrove Shoreline Affected by Water-Management Outfall Structures and Associated Endwall Projects per 5-Year Period

Table 37. USACE and NMFS Determinations on the Effects of Water-Management and Endwall Activities (Activity 4) on Designated Critical Habitat

Table 38. Estimated Amount of Waterbottom and Shoreline Areas Affected by Water- Management Outfall Structures and Associated Endwall Projects in Smalltooth Sawfish, Gulf Sturgeon, and Johnson’s Seagrass Critical Habitat

Table 39. USACE and NMFS Determinations on the Effects of Scientific Survey Device Activities (Activity 5) to ESA-listed Species Listed in Table 5

Table 40. Estimated Number of Scientific Survey Activities and the Associated Temporary Habitat Impacts over a 5-Year Period

Table 41. USACE and NMFS Determinations on the Effects of Scientific Survey Device Activities (Activity 5) to Designated Critical Habitat

Table 42. Estimated Number of Scientific Survey Device Projects and Associated Temporary Impacts in Critical Habitat with Effects Determinations

Table 43. USACE and NMFS Determinations on the Effects of Boat Ramp Activities (Activity

6) on ESA-listed Species Listed in Table 5

Table 44. Estimated Amount of Waterbottom Affected by from Boat Ramp per 5-Year Period

Table 45. USACE and NMFS Determinations on the Effects of Boat Ramp Activities (Activity

6) to Designated Critical Habitat

Table 46. Estimated Amount of Waterbottom Affected by Boat Ramp Activities in Smalltooth Sawfish, Gulf Sturgeon, and Johnson’s Seagrass Critical Habitat per 5-Year Period

Table 47. USACE’s Estimated Number of Aquatic Enhancement Projects per 5-year Period and the Anticipated Impacts per Project

Table 48. USACE and NMFS Determinations of the Effects of Aquatic Enhancement, Enhancement (Activity 7) on ESA-listed Species Listed in Table 5

Table 49. Estimated Amount of Waterbottom Affected by Aquatic Enhancement per 5-Year Period

Table 50. USACE and NMFS Determinations on the Effects of Aquatic Enhancement (Activity

7) to Designated Critical Habitat

Table 51. Maximum Area Supporting the Essential Features of Smalltooth Sawfish, Gulf Sturgeon, and Johnson’s Seagrass Critical Habitat that May Be Affected by Aquatic Restoration Projects per 5-Year Period

Table 52. USACE and NMFS Determinations on the Effects of Transmission and Utility Line Projects on ESA-listed Species Listed in Table 5

Table 53. Estimated Waterbottom Covered by Transmission and Utility Line Projects Per Project

Table 54. Estimated Potential Impacts to Areas Supporting the Essential Features of Smalltooth Sawfish, Gulf Sturgeon, and Johnson’s Seagrass Critical Habitat from Transmission and Utility Line Projects Per 5-Year Period

Table 55. USACE and NMFS Determinations on the Effects of Transmission and Utility Line Projects (Activity 8) on Designated Critical Habitat

Table 56. USACE and NMFS Determinations on the Effects of Marine Debris Removal Activities (Activity 9) to ESA-listed Species listed in Table 5

Table 57. USACE and NMFS Determinations on the Effects of Marine Debris Removal (Activity 9) to Designated Critical Habitats

Table 58. USACE and NMFS Determinations on the Effects of Temporary Platforms, Fill, and Cofferdam Activities (Activity 10) on Sea Turtles, Smalltooth Sawfish, and Sturgeon

Table 59. Estimated Amount of Waterbottom Affected by Temporary Platforms, Fill, and Cofferdam Activities in Florida and the U.S. Caribbean per 5-Year Period

Table 60. USACE and NMFS Determinations on the Effects of Temporary Platform, Fill, and Cofferdam Activities under (Activity 10) to Designated Critical Habitat

Table 61. Estimated Amount of Waterbottom Affected by Temporary Platform, Fill, and Cofferdam Activities under (Activity 10) in Smalltooth Sawfish, Gulf sturgeon, and Johnson’s Seagrass Critical Habitat per 5-Year Period

Table 62. Summary of NMFS Determination of Effects to Species by Activity Type

Table 63. Summary of NMFS Determination of Effects to Critical Habitat by Activity Type . 234

Table 64. Designated critical habitat units for Johnson's seagrass

Table 65. Impacts to Johnson’s Seagrass Anticipated per 5-year period

Table 66. Impacts to Johnson’s Seagrass Critical Habitat Anticipated per 5-year period270

Table 67. Impacts to Smalltooth Sawfish Critical Habitat Anticipated per 5-year period271

Table 68. Summary of Impacts to the Shallow, Euryhaline Habitat Essential Feature

Table 69. Summary of Impacts to the Red Mangrove Essential Feature

Table 70. NWPs used by the USACE Jacksonville District

Table 71. USACE General Permits in Florida and the U.S. Caribbean That May Affect Species within NMFS’ Jursidiction

Table 72. Hearing ranges of listed species

Table 73. Impact pile-driving threshold noise levels for fish and sea turtles

Table 74. Continuous noise threshold levels for fish and turtles from exposure to vibratory pile-driving noise

Table 75. Impact Hammer sound source levels and impact radius distances

Table 76. Vibratory Hammer sound source levels and impact radius distances

Table 77. Effectiveness and cost of noise control measures for pile driving

Table 78. Back-Calculation of Source Levels

Table 79. Calculations of Threshold Exceedances

Table 80. Calculations of Impact Zones Based on Source Levels for the Project

Acronyms and Abbreviations

ADA Americans with Disabilities Act AIWW Atlantic Intracoastal Waterway ATON Aid-to-Navigation

BMP Best Management Practice CHEU Charlotte Harbor Estuary Unit cSEL Cumulative Sound Exposure Level CWA Clean Water Act dB decibels dB re 1 μPa decibels relative to 1 micro-Pascal-squared second DPS Distinct Population Segment EFH Essential Fish Habitat EPA U.S. Environmental Protection Agency ESA Endangered Species Act FEMA Federal Emergency Management Agency FDEP Florida Department of Environmental Protection FKNMS Florida Keys National Marine Sanctuary FPL Florida Power and Light GIS Geographic Information System GIWW Gulf Intracoastal Waterway GP General Permit GRBO Gulf of Mexico Regional Biological Opinion ICW Intracoastal Waterway IP Individual Permit IPCC Intergovernmental Panel on Climate Change JAXBO Jacksonville District’s Programmatic Biological Opinion LAA Likely to Adversely Affect LOP Letters of Permission MHW Mean High Water MHWL Mean High Water Line MLLW Mean Lower Low Water MLW Mean Low Water MMPA Marine Mammal Protection Act N Number of Projects N/A Not Applicable NA DPS North Atlantic Distinct Population Segment NE No Effect NLAA Not Likely to Adversely Affect NMFS National Marine Fisheries Service NOAA National Oceanic and Atmospheric Administration NP Not Present NPS National Park Service NWA DPS Northwest Atlantic Distinct Population Segment NWP Nationwide Permit P Present PATON Private Aid to Navigation PBF Physical and Biological Feature PCE Primary Constituent Element PDC Project Design Criteria PGP Programmatic General Permit

PRD Protected Resources Division PVC Polyvinyl Chloride RGP Regional General Permit RHA Rivers and Harbors Act RM Red Mangrove RMS Root Mean Square SAJ South Atlantic Jacksonville SARBO South Atlantic Regional Biological Opinion SH Shallow, Euryhaline Habitat SEL Sound Exposure Level SFWMD South Florida Water Management District SP Standard Permit SPGP State Programmatic General Permit sSEL Single Strike Sound Exposure Level SWPBO Statewide Programmatic Biological Opinion TNAP Temporary Noise Attenuation Pile TTIEU Ten Thousand Islands/Everglades Unit USACE U.S. Army Corps of Engineers USCG U.S. Coast Guard USFWS U.S. Fish and Wildlife Service WCIND West Coast Inland Navigational District

Units of Measurement

Temperature °F degrees Fahrenheit °C degrees Celsius

Length and Area ac acre(s) cm centimeter(s) ft foot/feet ft² square foot/feet in inch(es) km kilometer(s) lin ft linear foot/feet m meter(s) m² square meter(s) mm millimeter(s) nmi nautical mile(s) nmi² square nautical mile(s)

Background Section 7(a)(2) of the Endangered Species Act (ESA) of 1973, as amended (16 U.S.C. §1531 et seq.), requires that each federal agency ensure that any action authorized, funded, or carried out by the agency is not likely to jeopardize the continued existence of any endangered or threatened species or result in the destruction or adverse modification of critical habitat of those species.

When the action of a federal agency may affect a protected species or its critical habitat, that agency is required to consult with either the National Marine Fisheries Service (NMFS) or the U.S. Fish and Wildlife Service (USFWS), depending upon the protected species or critical habitat that may be affected.

Consultations on most listed marine species and their designated critical habitat are conducted between the action agency and NMFS. Consultations are concluded after NMFS determines the action is not likely to adversely affect listed species or critical habitat or issues a Biological Opinion (“Opinion”) that determines whether a proposed action is likely to jeopardize the continued existence of a federally listed species, or destroy or adversely modify federally designated critical habitat. The Opinion also states the amount or extent of listed species incidental take that may occur and develops non-discretionary measures that the action agency must take to reduce the effects of said anticipated/authorized take. The Opinion may also recommend discretionary conservation measures. No destruction or adverse modification of critical habitat may be authorized. The issuance of an Opinion detailing NMFS’s findings concludes ESA Section 7 consultation.

This document represents NMFS’s Opinion based on our review of impacts associated with 10 categories of in-water activities that the USACE’s Jacksonville District authorizes under Section 10 of the Rivers and Harbors Act (RHA) of 1899 and Section 404 of the Clean Water Act (CWA) throughout Florida and the U.S. Caribbean, including:

1. Shoreline stabilization (e.g., installation, repair, and removal of structures)

2. Pile-supported structures and anchored buoys (e.g., installation, repair, and removal of structures)

3. Dredging including maintenance, minor, and muck dredging

4. Water-management outfall structures and associated endwalls1 (e.g., installation, repair, and removal of water outfall structures)

5. Scientific survey devices (e.g., installation, repair, and removal of structures)

6. Boat ramps (e.g., installation, repair, and removal of structures)

1 Endwalls are retaining walls at the end of the outfall structure that protect the area surrounding the outfall pipe from scouring.

7. Aquatic habitat enhancement, establishment, and restoration activities (oyster reef and living shorelines, seagrass restoration, artificial reefs, fill to restore natural contours or improve water quality)

8. Transmission and utility lines (e.g., installation, repair, and removal of aquatic and subaqueous lines)

9. Marine debris removal

10. Temporary platforms, fill, and cofferdams (e.g., installation, repair, and removal of structures)

We analyze the effects of these 10 categories of activities in Florida and the U.S. Caribbean on the endangered (E) and threatened (T) species and critical habitat under our jurisdiction, in accordance with Section 7 of the ESA. This Opinion is based on information provided by USACE and the best scientific and commercial data available.

Programmatic Consultations Programmatic consultations2 allow for streamlined review of groups of frequently occurring or routine activities or Federal action agency policies, plans, regulations or programs that have well-understood and predictable effects on ESA-listed species and designated critical habitat.3 Programmatic consultations can be used to evaluate the effects of authorizing certain categories of frequently occurring activities or of agency policy or programs, where specifics of any individual future project (either of the given category or type of activity, or occurring under the policy or program), such as the specific location, are not definitively known at the time of the programmatic consultation.

As is done in this Opinion, a Programmatic Consultation generally identifies project design criteria (PDCs), which are the specific criteria, including the technical and engineering specifications, indicating how an individual project must be sited, constructed, or otherwise carried out to avoid or minimize adverse effects to ESA-listed species or designated critical habitat. The PDCs serve 2 important purposes. First, they ensure that the actions under consultation are sufficiently similar that their effects can be analyzed together. Second, the PDCs help protect species and critical habitat, and ensure that the action agency is meeting its obligation under Section 7(a)(2); in designing the PDCs, NMFS and the action agency work to establish conditions that avoid adverse effects on listed species or designated critical habitat or, 2 It is important to note that the term “programmatic” is defined differently by NMFS when discussing a Programmatic Consultation or Programmatic Biological Opinion than it is by USACE when discussing a Programmatic General Permit (see Appendix A).

3 See, e.g., Joint Services memorandum, Alternative Approaches for Streamlining Section 7 Consultation on Hazardous Fuels Treatment Projects, https://www.fws.gov/endangered/esa-library/pdf/streamlining.pdf; 68 FR 1628 (January 13, 2003).

where the adverse effect cannot be avoided, to limit them to predictable levels that will not jeopardize the continued existence of listed species or destroy or adversely modify critical habitat either at the individual project level or in aggregate.

The Programmatic Consultation document evaluates the aggregate effect of categories of related actions or of the agency program. This includes the amount or extent of incidental take that is expected, if sufficient information exists to estimate take. Since programmatic consultations evaluate effects of expected future actions, the action agency must provide projections of the number of activities and the extent of expected effects from the proposed activities. The Programmatic Consultation document must demonstrate that, when the PDCs are followed, the aggregate expected effect of all projects is not likely to adversely affect listed species or their critical habitat(s), or will not jeopardize species or destroy or adversely modify their critical habitat(s), as applicable. At the project-specific consultation stage, each proposed action is reviewed to determine if it can be implemented according to the PDCs. For example, an action agency may certify that the expected effect of the project to be authorized is consistent with the PDCs and other conditions in the Programmatic Consultation. Adjustments to the project(s) may be necessary to bring them into compliance with the Programmatic Consultation document.

Finally, the project-specific consultation procedures provide contingencies for proposed projects that cannot be implemented in accordance with the PDCs; for example, separate consultations may be performed on these projects if they are too dissimilar from those described in the Programmatic Consultation document. In addition, the Programmatic Consultation must provide a process for tracking the actual effects of the proposed activities, once implemented, and ensure that the number and scope of the effects do not exceed those analyzed in the consultation or otherwise require reinitiation. NMFS generally conducts a programmatic-level review of the actual effects and compliance with the Programmatic Consultation on an annual basis.

The following elements, which generally are included in a Programmatic Consultation to ensure its compliance with ESA Section 7 and its implementing regulations, have been included in this Opinion:

1. Description of the proposed action, including the categories of similar projects under consultation (referred to as the Activities) and the PDCs applicable to all activities (general PDCs) and to the individual categories of activities (activity-specific PDCs) that are designed to avoid or minimize future adverse effects on listed species and critical habitat (Section 2.2).

2. Description of the manner in which the projects, when implemented consistent with the general and activity-specific PDCs, may affect listed species and critical habitat and evaluation of expected effects of the covered projects (Section 2.2). For each activity, we describe the process we used, in coordination with the action agency, to evaluate the expected effects, including the assumptions about the number and scope of each expected project. This Programmatic Opinion does not authorize any take.

3. Procedures for streamlined project-specific review, and the process for separate consultations for projects that do not meet the requirements of the Opinion (Section 2.3).

4. Procedures for monitoring projects and validating the predicted effects, and for the comprehensive review of the projects authorized in reliance on the Opinion as a whole (Section 2.4).

Consultation History 1

On December 14, 2015, the USACE requested a Programmatic Biological Opinion to address certain activities authorized under Section 10 of the RHA and Section 404 of the CWA in Florida. Consultation was initiated that day, though we continued to work with USACE to refine the proposed action. The original request was to address 11 categories of USACE-authorized activities. Through discussion with the USACE, the 11 categories of activities were reduced to 10 by combining 2 activities. In particular, we combined the reconfiguration and repair of existing docking facilities within a USACE-authorized marina with installation, repair, replacement, and removal of pile-supported structures and anchored buoys, since both categories primarily involve pile-supported structures. Additionally, this Opinion modifies some of the PDCs that the USACE included in its consultation request.

The USACE requested that this Opinion analyze activities authorized under its multiple existing and proposed general permits (GPs) in Florida. As explained below, the USACE had previously consulted with us on several of these GPs and this Opinion covers the activities authorized under 5 such permits, as noted below. Including the activities authorized under multiple GPs in this Opinion allowed us to review the majority of the minor in-water construction activities that the USACE permits in Florida under Section 10 of the RHA and Section 404 of the CWA, and to analyze the cumulative effects of these actions.

Once the USACE completes any process and other requirements (e.g., public notices or comment periods) necessary for full implementation, this Opinion will address the effects of activities authorized by the following renewals of existing GPs, and replaces and supersedes any prior consultations on the permits or prior iterations of these permits:

• Renewal of the Florida State Programmatic General Permit (SPGP). The USACE requested programmatic consultation on this renewal on August 26, 2015. We did not complete a separate programmatic consultation on that GP, but rather incorporated the actions authorized under that permit in this Opinion. The previous SPGP was evaluated through a Programmatic Opinion issued by NMFS on December 21, 2011 (SPGP IV-RI, SER-2011- 05980),

• Renewal of the 12 USACE South Atlantic Jacksonville (SAJ) District GPs, which were previously evaluated through a Programmatic Opinion issued by NMFS on December 19, 2012 (12 USACE SAJ General Permits, SER 2011-01939).

• Renewal of the GP SAJ-82, which was previously evaluated in a Biological Opinion issued by NMFS on June 10, 2014 (SER-2008-02958).

• Renewal of the Programmatic General Permit (PGP) SAJ-42, which was previously evaluated in a Biological Opinion issued by NMFS on February 10, 2011 (SER-2008-01790).

Additionally, this Opinion will supersede the Florida Statewide Programmatic Biological Opinion (SWPBO) issued by NMFS on December 4, 2015 (SER-2013-12540).

This Programmatic Opinion will not address the following completed or in progress consultations:

• Renewal of SAJ-99 (SER-2014-13378) or SAJ-71 (SER-2015-17183) used for the deposition of aquaculture materials.

• Completion of the proposed SAJ-112 for coral propagation and nursery structures off the Florida, Puerto Rico, and U.S. Virgin Islands (SER-2014-15282).

• South Atlantic Regional Biological Opinion (SARBO) (NMFS 1997) and the Gulf of Mexico

Regional Biological Opinion (GRBO) (NMFS 2007b), which both address federal actions associated with maintenance dredging.

In the SWPBO issued on December 4, 2015, we evaluated the USACE’s authorization of 11 categories of minor in-water activities under Nationwide Permits (NWPs) or Individual Permits (IPs). Although this Opinion includes the same categories of activities as SWPBO,4 it is broader than the SWPBO because it also considers those activities when authorized under USACE regional, general, and programmatic permits (i.e., it is not simply limited to authorization of those activities under USACE NWPs or IPs).

After working directly with the USACE to develop the updated PDCs for this Opinion, we sent a draft of the consultation history, descriptions of the actions, PDCs, and the assumptions that went into estimating the effects of the activities to the USACE on March 10, 2016. The USACE provided comments on March 17, 2016.

On November 14, 2016, the USACE requested programmatic consultation on 11 categories of activities associated with the proposed 2017 Nationwide Permits for work in Puerto Rico and the U.S. Virgin Islands.

On January 12 and 31, 2017, we met with the USACE to discuss expanding this consultation to include not only activities authorized under the proposed 2017 NWPs in Puerto Rico and the U.S. Virgin Islands, but also activities authorized under IPs within that area. Together with the USACE, we drafted and reviewed additional PDCs and we decided it was appropriate to expand the consultation. The USACE requested to consult on the same 10 categories of activities as

4 As we explained above, we have revised the description of the covered categories from 11 categories to 10 categories by combining “the reconfiguration and repair of existing docking facilities within a USACE-authorized marina” with “installation, repair, replacement, and removal of pile-supported structures and anchored buoys,” since both categories primarily involve pile-supported structures. Thus, although the SWPBO covered 11 categories of activities, and this Opinion covers 10, the Opinions discuss the same categories of actions.

analyzed in this Opinion, and an additional 11th category, aquaculture. NMFS and the USACE decided to not consult on aquaculture in this Opinion.

At the USACE’s request, we provided the USACE a draft of the entire document for review before we completed the consultation.

Description of the Proposed Action and Potential Routes of Effect to Species and 2 Critical Habitat

This Programmatic Opinion evaluates 10 categories of the most common, minor in-water activities that the USACE regularly authorizes in the state of Florida and the U.S. Caribbean under Section 404 of the CWA and Section 10 of the RHA. The USACE authorizes these activities using a variety of mechanisms including regional general permits (RGPs), PGPs, NWPs, and IPs. This Opinion does not cover all types of activities or projects that the USACE permits under its CWA or RHA authority, but instead focuses on those minor projects that the USACE regularly authorizes that have predictable effects. This Opinion does not directly link each activity to a specific USACE CWA or RHA permit (by which we mean we are not consulting on a particular RGP, PGP, or NWP). Instead, the Opinion focuses on the categories of activities authorized under the USACE’s CWA and RHA permitting authority and the effects those activities may have on species and critical habitat under NMFS’s purview.

The goal of this Opinion is to streamline and consolidate ESA Section 7 consultation for the majority of minor in-water coastal development activities that the USACE Jacksonville District authorizes in Florida and the U.S. Caribbean. In this Opinion, we are able to provide a more comprehensive and cohesive review of the majority of the minor in-water construction projects in Florida and the U.S. Caribbean that are permitted by the USACE under Section 10 of the RHA and Section 404 of the CWA and to analyze the cumulative effects of these actions, than if we consulted on a project-by-project basis.

Below, we provide a description of:

• How the Opinion may be used (described below)

• The areas in Florida and the U.S. Caribbean in which the permitted activities covered under this Opinion occur, including areas where additional restrictions apply (Section 2.1).

• The 10 categories of activities covered by this Opinion, including the PDCs those activities must meet to be covered (Section 2.2).

• An estimate of the number of activities that the USACE (or an entity with delegated authority from the USACE) will permit over a 5-year period that are covered by this Opinion (Section 2.2).

• The project-specific review (Section 2.3) and programmatic review (Section 2.4) requirements necessary to ensure that the reliance on this Opinion is limited to those actions in Florida and the U.S. Caribbean that meet the PDCs in this Opinion and are consistent with this Opinion.

Use of the Opinion As explained above, the USACE requested programmatic consultation on the effect of authorizing projects falling within 10 categories of activities occuring throughout the state of Florida and the U.S. Caribbean. The USACE determined that the 9 out of the 10 categories of activities may affect certain ESA-listed species or designated critical habitat within NMFS’s purview (all but Activity 9, marine debris removal; see Section 2.1.2 for the USACE’s effects determinations). NMFS believes that all of the activities described below, if carried out as described, will have effects on ESA-listed species and/or critical habitat as discussed herein. The USACE may rely on this Opinion to meet its ESA Section 7 consultation requirements when authorizing activities that meet the PDCs and other requirements of the Opinion. Nothing in this Opinion precludes the USACE from determining that a future project does not affect an ESA-listed species or designated critical habitat. NMFS and the USACE will continue to discuss the Opinion as it is applied, at the project-specific and programmatic reviews described in Sections

2.3 and 2.4, and may refine it in the future.

Two USACE Divisions, the USACE Regulatory Division and the USACE Civil Works Division, have responsibility for authorizing and/or implementing in-water projects under the CWA and the RHA and consulting on the effects of those projects under the ESA. Both Divisions can satisfy their ESA Section 7 requirements by relying on this Opinion for projects meeting the requirements of this Opinion.

In addition, entities to which the USACE has delegated certain CWA Section 404 and/or RHA Section 10 permitting authority—such as the Florida Department of Environmental Protection (FDEP), a water management district, or a local government with delegated authority under Section 373.441, F.S.—also may rely on this Opinion to satisfy their ESA Section 7 obligations, again, to the extent the authorized activities are consistent with the PDCs and the other requirements of the Opinion. Unless the USACE has negotiated with the entity otherwise, the delegated authority must submit information on its authorized projects under the project-specific review procedures set forth in Section 2.3 to both NMFS and the USACE, but NMFS will coordinate directly with the USACE on any issues raised during the project-specific review. The USACE remains responsible for the programmatic review, as set forth in Section 2.4.

The USACE also may share responsibility for authorizing the activities addressed in this Opinion with another federal action agency. When 2 or more federal agencies are involved in authorizing, funding, or carrying out an activity that may affect listed species or critical habitat, a single agency may be designated as the lead for consultation under Section 7 of the ESA, per the factors in 50 CFR 402.07, which include the “time sequence in which the agencies would become involved, the magnitude of their respective involvement, and their relative expertise with respect to the environmental effects of the action.”5 If a federal action agency other than the USACE has been designated the lead action agency for the Section 7 consultation on a project that fits within 1 or more of the activities covered under this Opinion, that agency may rely on this Opinion in meeting its ESA Section 7 requirements, as long as the USACE is part of the

5 50 CFR § 402.07 requires the lead agency to provide written notification of the designation to NMFS.

consultation and the project under consultation meets the PDCs and all other requirements of the Opinion, as described in the examples below. The USACE remains responsible for meeting the project-specific review and programmatic review requirements, according to the procedures outlined in Section 2.3 and 2.4 of this Opinion. Since the non-USACE federal action agency may be aware of a proposed project first, we suggest the non-USACE federal action agency contact the USACE early in the process to ensure that both federal action agencies have the necessary information from the applicant to complete both the ESA Section 7 requirements and their own permitting, funding, or other requirements.

For example, the following projects may require ESA Section 7 consultation coordination between the USACE and another federal action agency:

• The National Park Service (NPS) may wish to install a new aids-to-navigation (ATON). In addition to requiring authorization from USACE under Section 10 of the RHA, the NPS would need authorization from the U.S. Coast Guard (USCG). Both federal authorizations (USACE and USCG) would require Section 7 consultation and either the USCG or the USACE could be the lead action agency for the consultation. If the USCG was the lead action agency, and the USACE was a co-consulting action agency, the USCG could use this Opinion in satisfying its ESA Section 7 requirements; as long as the ATON met the general and activity-specific PDCs of this Opinion (ATONs fall within Category 2, below).

• The Federal Emergency Management Agency (FEMA) or the National Oceanic and Atmospheric Administration (NOAA) Restoration Division may request ESA Section 7 consultation on its action to fund 1 of the 10 categories of in-water work covered under this Opinion. As long as FEMA or NOAA Restoration Center’s action has a nexus to the Opinion—i.e., FEMA or NOAA Restoration is funding a project for which the applicant also must apply for a USACE permit for 1 of the 10 categories of activities covered under this Opinion—if FEMA or NOAA Restoration Center is designated as the lead federal action agency for Section 7 consultation, and the USACE was a co-consulting action agency, FEMA or NOAA Restoration Center may rely on the Opinion.

In the federal coordination examples above, the USACE remains responsible for meeting the project-specific review and programmatic review requirements, according to the procedures outlined in Section 2.3 and 2.4 of this Opinion. Throughout the Opinion, we use the term USACE to refer to the USACE or any entity that is taking the lead for or otherwise responsible for the Section 7 consultation as described above, unless otherwise noted.

This Opinion may not be used to consult on 1 portion of a larger project. In order to rely on this Programmatic Opinion to meet the ESA Section 7 consultation requirements, all of the activities within the project must be covered under this Opinion and must meet the PDCs of the Opinion, unless all aspects of the project have been considered and are covered under this Opinion and other programmatic opinions. For example, the USACE could rely on this Opinion for its decision to issue a permit allowing for construction of a dock and seawall and for minor dredging if all of the general PDCs and all of PDCs for those specific activities (the docks, seawalls, and minor dredging) were met. However, if 1 activity did not meet the PDCs, then the USACE would have to consult on the entire project with NMFS separately via an individual consultation.

For example, if the seawall did not meet PDC A.1.1.1 because it was greater than 500 ft in length, then the USACE would have to request an individual consultation that covers all components of the project. The USACE could not rely on this Opinion to consult on the minor dredging and the dock, and separately consult on the seawall. However, if all aspects of the project are covered in 2 or more programmatic opinions, the USACE may rely on those opinions and need not seek individual consultation on the project. NMFS expects this Opinion may be used in combination with the upcoming Programmatic Opinion on the Effects of Research, Restoration, and Relocation on Threatened Caribbean Corals (referred to as the 3Rs Programmatic Biological Opinion, NMFS tracking number SER-2016-18298). For example, if a project covered under this Opinion had coral onsite that was removed prior to starting construction, the coral relocation would be covered under the 3Rs Programmatic Biological Opinion and the construction of the project would be covered under this Opinion.