# Revised Biological Assessment f or Designation

of a n Ocean Dredged Material Disposal Site

o ff Jacksonville, Florida

January 2015Appendix C: Biological Assessment

i 

## TABLE OF CONTENTS

1. INTRODUCTION

................................ ................................ ................................ .......... 1

1.1. Purpose and Need for Proposed Action

................................ ................................ .. 1

1.2. Description of Action Area

................................ ................................ ..................... 3

1.3. Listed and/or Proposed Species or Critical Habitat Within the Action Area

................. 3

2. DESCRIPTION O F LISTED SPECIES AND CRITICAL HABITAT THAT MAY BE AFFECTED BY THE PROPOSED ACTION

................................ ................................ .... 5

2.1. Sea Turtles

................................ ................................ ................................ .......... 5

2.1.1. Logge rhead Sea Turtle

................................ ................................ .......... 5

2.1.2. Kemp’s Ridley Sea Turtle

................................ ................................ ....... 6

2.1.3. Green Sea Turtle

................................ ................................ ................... 7

2.1.4. Leatherback Sea Turtle

................................ ................................ .......... 8

2.2. Marine Mammals

................................ ................................ ................................ .. 8

2.2.1. North Atlantic Right Whale

................................ ................................ ...... 8

2.2.2. Humpback Whale

................................ ................................ ................. 14

2.3. Fish

................................ ................................ ................................ .................. 14

2.3.1. Shortnose S turgeon

................................ ................................ .............. 14

2.3.2. Smalltooth Sawfish

................................ ................................ ............... 15

2.3.3. Atlantic Sturgeon

................................ ................................ .................. 15

3. EFFECTS OF PROPOSED ACTION

................................ ................................ ............. 18

3.1. Sea Turtles

................................ ................................ ................................ ......... 19

3.2. Marine Mammals

................................ ................................ ................................ . 19

3.3. Fish

................................ ................................ ................................ .................. 20

3.3.1. Shortnose a nd Atlantic Sturgeon

................................ ............................ 20

3.3.2. Smalltooth Sawfish

................................ ................................ ............... 20

4. MEASURES TO AVOID, MINIMIZE, AND COMPENSATE FOR EFFECTS

...................... 23

4.1. Sea Turtles

................................ ................................ ................................ ......... 23

4.2. Marine Mammals

................................ ................................ ................................ . 23

5. CUMULATIVE EFFECTS ANALYSIS

................................ ................................ ............ 24

6. CONCLUSION

................................ ................................ ................................ ............ 27

7. LITERATURE CITED

................................ ................................ ................................ ... 29

8. LIST OF PREPARERS

................................ ................................ ................................ 33Appendix C: Biological Assessment

ii 

## FIGURES

Figure 1

- 1 Region of Interest Showing Proposed Alternatives and Existing Jacksonville

and Fernandina Ocean Dredged Material Disposal Sites

................................ ....... 2 Figure 2

- 1 North Atlantic Right Whale Migration Patterns

................................ ..................... 10 Figure 2

- 2 North Atlantic Right Whale Critical Habitat

................................ ........................... 11 Figure 2

- 3 North Atlantic Right Whale Occurrences within the Region of Interest

................. 12 Figure 2

- 4 Whale Strandings within the Project Area (1991

- 2006)

................................ ........ 13 Figure 2

- 5 FWRI Right Whale Sightings 2008

- 2009

................................ .............................. 14 Figure 2

- 6 Range of the Atlantic Sturgeon

................................ ................................ ............ 18



## TABLES

Table 1

- 1 ESA

- Listed Species and Critical Habitat under the Jurisdiction of NMFS

Potentially Occurring within the Action Area

................................ ........................... 4
Table 2

- 1 Sea Turtle Nesting Data for Duval County, Florida (1990

- 20 11 )

............................ 6
Table 3

- 1 Summary of the Potential Direct and Indirect Effects on ESA

- Listed Species

...... 19
Table 6

- 1 Summary of Effects on Listed Species and Critical Habitat

................................ .. 27Appendix C: Biological Assessment

iii 

## ACRONYMS AND ABBREVIATIONS

ASMFC Atlantic States Marine Fisheries Commission
ASSRT Atlantic Sturgeon Status Review Team

BA biological assessment
CDF confined disposal facility
CEQ Council of Environmental Quality

cy cubic yards
DoN Department of the Navy
DPS Distinct Population Segment
EIS Environmental Impact Statement
EPA/USEPA U.S. Environmental Protection Agency
ESA Endangered Species Act
EWS early warning system
FWC Florida Fish and Wildlife Conservation Commission

FWRI Fish and Wildlife Research Institute

MLLW mean lower low water

NARW North Atlantic right whale
NARWC North Atlantic Right Whale Consortium
NAVFAC Naval Facilities Engineering Command

NEPA National Environmental Policy Act
NMFS National Marine Fisheries Service

nmi nautical mile(s)
ODMDS ocean dredged material disposal site
ROI region of influence
SARBO South Atlantic Regional Biological Opinion
SRT Status Review Team
USACE U.S. Army Corps of Engineers USEPA, EPA U.S. Environmental Protection Agency
USFWS U .S. Fish and Wildlife Service
USGS U.S. Geological SurveyAppendix C: Biological Assessment

iv This page intentionally left blank.Appendix C: Biological Assessment

1 

## 1. INTRO DUCTION

The U.S. Environmental Protection Agency Region 4 (EPA) proposes to designate a new or expanded ocean dredged material disposal site (ODMDS) offshore of Jacksonville, Duval County, Florida. Section 7 of the Endangered Species Act (ESA) requires federal agencies to ensure that any action is not likely to jeopardize the continued existence of any endangered or threatened species, including destruction or adverse modification of these species’ critical habitat s

. This Biological Assessment (BA) has been prepared in accordance with S ection 7 of the ESA to analyze potential impacts to nine species under the jurisdiction of the National Marine Fisheries Service (NMFS) known to occur within the action area

.


## 1.1. Purpose and Need for Proposed Action
The existing Jacksonville ODMDS is located approximately 5 nmi southeast of the mouth of the St. Johns River on the continental shelf off the east coast of Florida ( Figure 1

- 1 ) . It is 1 nmi by 1 nmi (1 nmi 2 ) in size and is the primary site for placement of dredged material originating from the Jacksonville Harbor Federal Navigation Project and Naval Station Mayport

. Due to capacity issues at this site, the U.S. Army Corps of Engineers Jacksonville District ( USACE ) and EPA have identified a need to either expand the existing Jacksonville ODMDS or designate a new ODMDS in the vicinity. The need for expanding current ocean disposal capacity is based on observed mounding, future capacity modeling, historical dredging volumes, lack of upland confined disposal facilities (CDF)

, and estimates of future proposed projects.

The purpose of the proposed a ction (designation of an ODMDS) is to ensure that adequate environmentally acceptable and economically and logistically feasible ocean disposal site capacity is available for the next 50 years for suitable dredged material generated from new projects and maintenance dredging in the vicin ity. This site will be used for the disposal of suitable dredged material originating in the Duval County region that is in compliance with the Ocean Dumping Criteria (40 CFR 227)

. Th e availability of suitable ocean disposal sites to support ongoing main tenance and capital improvement projects is essential for the continued use and economic growth of vital commercial and recreational areas in the region. As part of the site designation process, initial screening of alternative sites based on environmenta l, operational, and economic criteria were conducted to identify viable alternative sites that were evaluated in more detail during the site designation studies

. These alternatives are described in detail in Chapter 2 of the Environmental Impact Statement (EIS). The EIS evaluates the potential physical, chemical, biological, and socioeconomic impacts associated with the proposed designation of the new ODMDS offshore of Jacksonville , Florida. The alternatives considered in th e EIS and in this BA include t he expansion of the existing Jacksonville ODMDS (Alternative 1 a ), designation of a new site south of the Jacksonville ODMDS (Alternative 2), designation of a new site north of the Jacksonville ODMDS (Alternative 3), and the No Action Alternative (Figure 1

- 1).Appendix C: Biological Assessment

2Appendix C: Biological Assessment

3 

## 1.2. Description of Action Area

The action area (or region of influence [ROI]) is defined as the geographic area in which listed species could potentially be affected by the proposed action

. Since v essels will be transiting between the St. Johns River and the designated site during dredged material disposal activities

, the marine habitats inshore of the alternatives sites are also considered in this assess ment. The refore, th e action area includes marine areas in the vicinity of the alternative sites (Figure 1

- 1).

The three alternative sites are situated on the inner continental shelf from approximately 6.7 to 9.3 nmi from the mouth of the St. Johns River. Depths range fro m approximately 43 to 66 feet mean lower low water (MLLW). The ocean bottom is characterized by sand ridges and regular and irregular large

- scale bedforms as evidenced in sidescan imagery collected in October 2009 and March 2010, suggesting varying hydrod ynamic influences, including tidal, longshore, and storm

- derived currents. The bottom substrate is predominantly fine and medium quartz sand with fine shell fragments and traces of silt. Discrete areas of hardbottom are present near the existing Jacksonv ille ODMDS and appear as isolated piles and some more dispersed limestone material, ranging from pebble

- to boulder

- sized. The shape, pattern, and distribution of these features, along with historical use of the ODMDS to the south and east of existing bou ndaries, suggest that they are from prior disposal events. Hardbottom ledges and patchy low

- relief reefs are present to the east of Alternative 3. Hardbottom habitats within and adjacent to each alternative site were ground truthed and mapped. For a more detailed discussion of these habitats, see Final Report and Addendum to Final Report

– Jacksonville ODMDS Reconnaissance Sidescan Sonar Survey (ANAMAR 2010).



## 1.3. Listed and/or Proposed Species or Critical Habitat Within the Action Area

Based on t he species lists reviewed by NMFS, nine species listed under the ESA as endangered and threatened under the jurisdiction of NMFS potentially occur within the action area (Table 1

- 1) (NMFS 2010a)

. In addition, critical habitat has bee n designated for the North Atlantic right whale and loggerhead sea turtle . The BA addresses the potential impacts of designating a new or expanded ODMDS offshore of Jacksonville , Florida on these federally listed species and critical habitat. This BA is based upon literature review; data from NMFS, the U.S. Fish and Wildlife Service (USFWS), the Florida Fish and Wildlif e Conservation Commission (FWC); and previous agency consultations on similar projects in the vicinity such

as Final EIS for the Proposed Homeporting of Additional Surface Ships at Naval Station Mayport, Florida (NAVFAC 2008).Appendix C: Biological Assessment

4 Table 1

- 1. ESA

- Listed Species and Critical Habitat under the Jurisdiction of NMFS

Potentially Occurring within the Action Area

Common Name Scientific Name Status

SEA TURTLES
Loggerhead sea turtle Caretta caretta Threatened ; critical habitat

Green sea turtle Chelonia mydas Endangered/Threatened 1
Kemp’s ridley sea turtle Lepidochelys kempii Endangered

Leatherback sea turtle Dermochelys coriacea Endangered

MARINE FISH
Shortnose sturgeon Acipenser brevirostrum Endangered

Atlantic sturgeon

– South Atlantic DPS Acipenser oxyrinchus oxyrinchus Endangered

Smalltooth sawfish Pristis pectinata Endangered

MARINE MAMMALS

North Atlantic right whale Eubalaena glacialis Endangered; critical habitat designated 2

Humpback whale Megaptera novaeangliae Endangered

1 Green turtles in U.S. waters are listed as threatened except for the Florida breeding population, which is listed as endangered.

2 Based on the 2006 relisting of separate right whale species in the northern Pacific and northern Atlantic oceans, NMFS is in the process of re

- designating critical habitat for the North Atlantic right whale. A proposed critical habitat rule for the North Atlantic right whale (NARW) has been submitted to the Federal Register

. As of March 2014 , no ruling has been made.
Source: NMFS 2010 aAppendix C: Biological Assessment

5 

## 2. DESCRIPTION OF LISTED SPECIES AN D CRITICAL HABITAT THAT MAY BE AFFECTED BY THE PROPOSED ACTION

A total of nine threatened, endangered , or proposed endangered species under the jurisdiction of the NMFS potentially occur within or in the vicinity of the action area (Ta ble 1

- 1 )

. Th is section describes these species and th eir associated critical habitat.



## 2.1. Sea Turtles

2.1.1. Loggerhead Sea Turtle Loggerhead sea turtles have a wide distribution including the Atlantic, Pacific

, and Indian

oceans

. Loggerheads nest in the temperate and subtropical regions of their geographic distribution, and in the U.S. the most common nesting areas include the coastal region between North Carolina and Florida, including the Florida Gulf coast

. In the southeastern U.S., the nesting season for logg erheads is late May through early September

. Females lay approximately five nests annually on high

- energy beaches characterized as narrow and steeply sloped with coarse

- grained sand

. There is a 2

- month incubation period after which eggs hatch, resulting in births from June through November

. Hatchlings struggle through the surf and attempt to swim away from land until they are able to take refuge in the downward current of surface water of the ocean

. Several months are often spent in these nursery areas until ocean currents move the young turtles f a rther offshore to grow

. A pelagic existence can last between 7 and 12 years for juveniles before migration back to nearshore coastal areas to mature until adulthood

. Western North Atlantic adult loggerheads f orage predominately in areas throughout the relatively shallow continental shelf waters of the U.S., Bahamas, Cuba, and the Yucatán Peninsula, Mexico

. Adults migrate between foraging habitats and beaches for nesting along the continental shelf or long dis tances across oceanic waters ( NMFS and USFWS 1993; DoN 2002)

. The loggerhead turtle was listed as threatened in 1978 (NMFS 1978) , and t here are concerns for this species due to numerous human activities that impact nesting areas including alterations of beaches, such as beach armoring to prevent erosion for beachfront development or beach nourishment to replace sand lost to natural erosion

. Adult mortality can be caused by a number of factors, including, but not limited to

, coastal development that dest roys foraging habitat and numerous types of fisheries that involve bycatch (NMFS and USFWS 1993)

. Although populations appear to be rebounding in some areas of their distribution, this is not the case in all

areas

. Data collected by USFWS indicated a ste ady and steep decline in the number of nests sighted in Florida from 1998 through 2007 ( NMFS and USFWS 2007a )

. NMFS has determined that the loggerhead turtle has nine distinct population segments (DPS s )

. As of 201 1

, four DPSs

are listed as threatened and five are listed as endangered , including t he northwest Atlantic Ocean DPS ( http://www.nmfs.noaa.gov/pr/species/turtles/loggerhead.htm , accessed 2/27/12)

. Approximately 90% of all loggerhead nesting in the continental U.S. takes place in Florida (FWRI 2007 a )

. The 2011 FW C Index Nesting Beach Survey results indicate loggerhead nest counts on Florida's index beaches have declined from a peak of nearly 60,000 in 1998. A detailed analysis of Florida's long

- term loggerhead nesting data (1989

- 2011) revealed that following a 24 % increase between 1989 and 1998, nest counts declined 16 % between 1998 and 2011. However, the recent trend may be stabilizing. Loggerhead sea turtle nest

cou nts in 2011 were close to the average for the preceding 5

- year period ( http://myfwc.com/research/wildlife/sea

- turtles/nesting/beach

- survey

- totals/ , accessed 2/27/12). I n Duval County, nesting totals have fluctuated

, but have shown an overall increase between 1990Appendix C: Biological Assessment

6 and 20 11

. Table 2

- 1 contains 1990 to 20 11 nesting data for loggerhead, leatherback, and green sea turtles in Duval County.

The beaches inshore of the action area are habitat for loggerhead nesting, and the nearshore areas are sufficient for pelagic juvenile habitat and adult feeding activities (NAVFAC 2008). Loggerheads are the most commonly sighted sea turtles off the Atlantic coast of north Florida (DoN 2002) and are expected to occur in the vicinity of the alternative sites throughout the year

.

Table 2

- 1

. Sea Turtle Nesting Data for Duval County, Florida (1990

- 20 11 )

Year Loggerhead Leatherback Green
1990 43 0 0
1991 40 0 0
1992 29 0 0
1993 30 1 0
1994 78 0 0
1995 54 0 0
1996 69 0 0
1997 63 0 0
1998 72 1 2
1999 119 2 0
2000 80 0 1
2001 87 1 0
2002 55 0 0
2003 88 2 0
2004 41 0 1
2005 67 0 3
2006 103 0 4
2007 36 2 0
2008 99 1 1
2009 81 5 0
2011 152 3 3

1990

- 2006 data sources: FWRI 2007a,c,d 2007

- 20 11 data source: FWRI 201 1

Critical habitat was designated for loggerhead se a turtles July 10

, 2014 along the At lantic coast. Critical habitat identified as LOGG

- N

- 14, nearshore reproductive

, is located in the coastal area of the project location

. The boundaries of the unit are nearshore areas from the south boundary of Kathryn Abbey Hanna Park to Matanzas Inlet (crossing St. Augustine Inlet) from the mean high water line seaward 1.6 km (1 nmi ). The physical biological feature of nearshore reproductive habitat is defined as a portion of the nearshore waters adjacent to nesting beaches that are used by hatchlings to egress to the open

- water environment as well as by nesting females to transit be tween beach and open water during the nesting season. The primary constituent elements that support this habitat are the following: (1) nearshore waters directly off the highest density nesting beaches and their adjacent beaches as identified in 50 CFR 17.95 (c) to 1.6 km (1 mile) offshore; (2) waters sufficiently free of obstructions or artificial lighting to allow transit through the surf zone and outward toward open wa ter; and (3) waters with minimal manmade structures that could promote predators (i.e., nearshore predator concentration caused by submerged and emergent offshore structures), disrupt wave patterns necessary for orientation, and/or create excessive longsho re currents.Appendix C: Biological Assessment

7 

### 2.1.2. Kemp’s Ridley Sea Turtle

The historic distribution of the K emp’s ridley sea turtle includes the Gulf coasts of Mexico and the U.S. and the Atlantic coast of North America

. Kemp’s ridley sea turtles are shallow

- water benthic feeders often found foraging in embayments

. They nest in large aggregations called arribadas, which are speculated to enhance survival of eggs due to “safety in numbers

. ” The majority of nesting activities occur s in one isolated area of Mexico, with limited nesting

oc currences reported in Texas and no nesting occurrences recorded on the Atlantic coast of the U.S. ( NAVFAC 2008 )

. Kemp’s ridley populations have declined more than any other sea turtle species and was listed as endangered in 1970 (NMFS and USFWS 1992a ; 200 7 a ).

From 1979 through 2006 there were no records of Kemp’s ridley nesting in Duval County (FWRI 2007 b )

. Part of the post

- juvenile distribution include s the Atlantic coast through Florida, and occurrence is mainly seasonal for feeding

. The shallow water s of the southeast ern U.S. are suitable habitat for all life stages of this species throughout much of the year

, and Kemp’s ridley sea turtles are expected to occur year

- round in waters between the shoreline and the 50

- meter isobath

. The waters off the Atlantic coast of north Florida , including the alternative sites, are most suitable for Kemp’s ridley sea turtles from May through October ( DoN 2002)

.



### 2.1.3. Green Sea Turtle

Green sea turtles are distributed throughout the world’s oceans, and in the Western A tlantic they range from Massachusetts to Argentina, including the Gulf of Mexico and the Caribbean

. In the summer when water is warmer the distribution is broad, but in general these animals are not found north of Cape Hatteras along the Atlantic coast

. For U.S. populations, nesting occurs primarily in the U.S. Virgin Islands, Puerto Rico, and the Atlantic coast of Florida

. Nesting season takes place from April through September with an incubation period of approximately 2 months

. Because green sea turt les are herbivores and feed primarily on sea grasses and algae, adults are found in nearshore areas

. Juveniles are found more offshore rafting in algae and leading a pelagic existence until adulthood

. The green turtle was protected under the ESA in 1978, with breeding populations in Florida, the Pacific Ocean

, and Mexico listed as endangered and all others as threatened

. Current threats include loss of nesting habitat, death

as fisheries bycatch, and poaching

. A status review of the endangered nesting p opulations recommended that the populations remain listed as endangered, as currently there is not evidence that these populations have recover ed ( NMFS and USFWS 2007b ).

Green turtle nest counts have increased approximately tenfold from 1989 to 2011, a trend that differs markedly from that of the loggerhead. The nest count in 2011 was the highest for that period ( http://myfwc.com/research/wildlife/sea

- turtles/nes ting/beach

- survey

- totals/

, accessed 2/27/12). Although green sea turtles are known to nest in substantial numbers in the southeast U.S., in Florida they typically nest along the beaches from Brevard County south to Broward County, south of the action area ( DoN 2002)

. However, they do nest in very low numbers along the beaches of Duval County

. In 20 11

, three green turtle nests were recorded in Duval County (Table 2

- 1 ) ( FWRI 2011 )

. South of North Carolina, green sea turtles are expected to occur year

- round in waters between the shoreline and the 50

- m eter isobath

. The preferred habitats of this species are seagrass beds and worm

- rock reefs, which are located primarily in shallow water environments along the Atlantic coast

. Green sea turtles are e xpected to occur within the vicinity of the alternative sites throughout the year

.Appendix C: Biological Assessment

8 

### 2.1.4. Leatherback Sea Turtle Leatherback sea turtles are broadly distributed throughout the Atlantic, Pacific, and Caribbean Oceans and the Gulf of Mexico, with a relatively high tolerance for extreme temperatures

. This high temperature tolerance allows for long migrations through areas with varying oceanographic conditions ( DoN 2002)

. In addition to extreme thermal tolerances, leatherbacks are known to be deep divers (over 300 f ee t) and spend a large amount of time offshore in deeper waters (Eckert et al

. 1989)

. The hypothesized reason for the offshore preference is that leatherback sea turtles feed on jellyfish and other pelagic animals that are found most commonly offshor e (Eckert 1995)

. Although generally a deep

- diving pelagic species, seasonal movement into coastal waters to feed on large jellyfish that are associated with rivers and frontal boundaries has been documented

. Leatherback sea turtles nest from March throug h July, with an incubation period of 55 to 75 days ( DoN 2007a )

. The majority of nesting occurs along the coasts of Mexico, but nesting also occurs at various Caribbean locations and the Atlantic coast of Florida (Conley and Hoffman 1987)

. The leatherback sea turtle was listed as endangered in 1970 (NMFS and USFWS 1992 b )

. The decline in numbers of leatherback sea turtles is mainly attributed to nesting habitat degradation ; illegal harvest of adults and eggs ; incidental take such as by

- catch, entanglement, and dredging

- related takes; and pollution (Eckert 1995).

Surveyors counted a near

- record number of leatherback nests on index beaches in Florida in 2011. Similar to the nest counts for green turtles, leatherback nest counts have been increasing exponentially. From 1989 through 2011, leatherback nests at core i ndex beaches numbered from 27 to 615 ( http://myfwc.com/research/wildlife/sea

- turtles/nesting/beach

- survey

- totals/

, accessed 2/27/12). Leatherbacks typically nest a long the beaches from Brevard County south to Broward County, south of the vicinity of the action area

. However, they do nest in very low numbers along the beaches of Duval County

. In 2011

, three leatherback turtle nests were recorded in Duval County (Ta ble 2

- 1 ) (FWRI 20 11 )

. Leatherbacks are the second most commonly seen sea turtle, after loggerheads, off the Atlantic coast of north Florida (DoN 2002) and are expected to occur within the vicinity of the alternative sites th roughout the year.



## 2.2. Marine Mammals

2.2.1. North Atlantic Right Whale The historic range of the North Atlantic right whale (NARW) was from temperate areas to subarctic locations in the North Atlantic Ocean ( NAVFAC 2008 )

. Some individuals have been sighted migrating over extremely deep waters, but most sightings occur in coastal and continental shelf waters

. Individuals have been reported as far south as the Gulf of Mexico, although these occurrences are rare

. Currently, their distribution is highly influenced by season and specific ac tivities

. Calving occurs between November and April in s outheast ern U.S

. waters

. The coastal waters off Georgia and northern Florida are the only known calving ground for the North Atlantic right whale , with calving occurring between December and March ( Figure 2

- 1 ) (DoN 2007b )

. Feeding primarily occurs from spring until fall in coastal waters of the northeast ern U.S. and Canada where their prey (zooplankton) is abundant

. When North Atlantic right whale s are not occupied with reproductive or paternal duties, their distribution is strongly linked to the distribution of their prey , which is comprised of various zooplankton species, particularly those with high lipid content

. Migration for feeding is a crit ical activity, as both the quality and quantity of their food source are importan t

. Although general distributional patterns do exist, information for many individuals throughout the winter is not well documented (NMFS 2004, 2006 a ).

Ship collisions and e ntanglement in fishing gear are the primary causes of injury and death in the population

. According to the NMFS Large Whale Ship Strike Database, as of 2004, NorthAppendix C: Biological Assessment

9 Atlantic right whale s were the fourth most commonly struck whale species in the world

. The region comprised of the southeast ern U.S. and Caribbean had the fifth highest number of vessel strikes on all whale species in the world and was the leader in vessel strikes for all of North America

. When speed was recorded for individual vessel strike events, the most common vessel speed was 13 to 15 knots

. Substantially fewer strikes occurred for vessels traveling at speeds less than 10 knots (Jensen and Silber 2004)

. Additional factors such as habitat degradation, contaminants, predators, and past w haling activities have all contributed to the endangered status of the North Atlantic right whale (NMFS 2007b)

. Of particular concern are dredging activities, as individuals have been sighted in shipping channels and other areas where dredging is common

. This has led to agencies encouraging dredging operations to adopt protective measures, such as posting lookouts on hopper dredge vessels and adherence to recommended precautionary guidelines for operations to reduce the ri sk of collision (NMFS 2004 )

.

A ccording to the 20 11 North Atlantic right whale report card released annually by the North Atlantic Right Whale Consortium (NARWC) , the best estimate of catalogued North Atlantic right whale population was 4 90 individuals (NARWC 20 11 ). Even though population estimates are extremely low, there is hope that the population may rebound if effective actions are taken to reduce the number of collisions with ships and entanglements with fishing gear are effective (NMFS 2004 )

. The designation o f critical habitat is a means to minimize these activities in areas where North Atlantic right whale s are frequent ly present

. Designated critical habitat, which is the core of the calving ground and essential to the conservation of this species, is shown in Figure 2

- 2

. Critical habitat was designated in 1994 for the coastal areas of southern Georgia and northern Florida from shore out to 15 nmi offshore from the mouth of the Altamaha River, Georgia, to Jacksonville, Florida, and then from shore out 5 nmi offshore from Jacksonville to approximately Sebastian Inlet, Flo rida (NMFS 1994)

. Revision of the existing critical habitats has been under study for several years. NMFS is evaluating potential critical habitat areas along the entire Atlantic seaboard f rom Maine through Florida.

As shown in Figure 2

- 3 , based on annual surveys from December through March 1985 to 2007, North Atlantic right whale s are relatively common within the vicinity of the alternative sites , the area that would be transited between the dredge project area and the ODMDS, and near the federal navigation channel (Zani et al. 2006 , 2008 ; DoN 2007c ; Right Whale Consortium 2007)

. Coastal waters of Florida were identified as one of five “high use” areas in the revised NMFS recovery plan (NMFS 2004a)

. Figure 2

- 4 shows documented strandings of right whales in the vicinity of the project area between 1991 and 2006

. Figure 2

- 5 shows r ight whale sightings in the region of the project area from surveys conducted from 2008 to 2009 (FWRI 2009 )

. The eastern portion of the federal navigation channel and the three alternative sites are within North Atlantic right whale critical habitat.Appendix C: Biological Assessment

10Appendix C: Biological Assessment

11Appendix C: Biological Assessment

12Appendix C: Biological Assessment

13Appendix C: Biological Assessment

14 

### 2.2.2. Humpback Whale Humpback whales are found in all of the world’s oceans and were listed as endangered in 1973. In general, summers are spent at high

- latitude feeding grounds from southern New England to Norway, and migration during the winter is to the West Indies, over shallow banks and along continental coasts, where calving occurs. Most humpback whale sightings are in nearshore and continental shelf waters; however, humpback whales fre quently travel across deep water during migration. Calving peaks from January through March, but some animals have been documented arriving as early as December, and a few not leaving until June. Strandings occur each year, for which over 50% of the anim als exhibit scarring or fresh wounds due to fishing gear entanglement or boat collisions (DoN 2002).

Since humpback whales migrate south to calving grounds during the fall and make return migrations to the northern feeding grounds in spring, they are no t expected off the coast of Florida during the summer, when they will be at their northern feeding grounds. The coastal region of Florida is not designated as an area of concentrated occurrence for this species (DoN 2002). Humpback whales have been spott ed in the St. Johns River as recently as 2003. However, t he habitat in the action area is not ideal for foraging or breeding humpback whales, but would serve as a migration corridor to feeding and breeding grounds. Based on sightings, strandings, and lif e history characteristics, humpbacks are expected to occur occasionally within the offshore areas near the alternative sites during fall, winter, and spring (DoN 2002).



## 2.3. Fish

2.3.1. Shortnose Sturgeon Historical distribution for shortnose sturgeon has been in major rivers along the Atlantic seaboard, with the northern limit near the St. John River in Canada and the southern limit near the Indian River in central Florida ( NAVFAC 2008 )

. This species is known to spawn in freshwater rivers and feed and overwinter in freshwater and marine habitats, although occurrence in the marine environment is less common

. Adults are generally thought to be estuarine anadromous in southern rivers

. Shortnose sturgeon were listed as an endangered species in 1967 and remained list ed with the passing of the ESA of 1972

. A recovery plan was completed for shortnose sturgeon in hopes to de

- list and recover populations depleted by habitat loss, fishing, and incidental fisheries bycatch

. Currently 19 populations of shortnose sturgeon h ave been identified throughout their distribution areas , and the only viable population south of Cape Hatteras, North Carolina

, resides in the Alta maha River

. Population dynamics information is virtually nonexistent for most southern populations due to th e small number of individuals recorded in surveys

. Shortnose sturgeon feed on crustaceans, insect larvae, worms,

an d mollusks (NMFS 1998).

Beginning in spring 2001, the Florida Fish and Wildlife Research Institute (FWRI) and the USFWS began research on the population status and distribution of the species in the St. Johns River

. After approximately 4,492 hours of gill

- net sampling from January through August of 2002 and 2003 in the upper river and estuarine area, only one shortnose sturgeon was captured

. In addition, after 21,381 hours of gill

- net sampling for other species from 1980 through 1993, there were no incidental captures of sturgeon

. Shortnose sturgeon are known to

use warm

- water springs in other southern rivers, but only eight individual fis h have been observed in the numerous warm

- water springs found upstream in the St. Johns River system, and these sightings occurred in the 1970s and early 1980s

. FWRI concluded that with the lack of current sightings in surveys, the patchy and extremely in frequent catch of small individuals, and the historic low numbers, it is highly unlikely that a significant population of shortnoseAppendix C: Biological Assessment

15 sturgeon currently resides within the St. Johns River (FWRI 2007 e )

. Because the St. Johns River is heavily industrialized a nd has been for many years, shortnose sturgeon populations may have suffered due to habitat degradation and blocked access to historic spawning grounds in the upstream reaches of the river

. Spawning habitat for this species is rock or gravel substrate nea r limestone outcroppings, which is very rare in the St. Johns River and associated tributaries

. Reproduction of shortnose sturgeon has not been documented in the St. Johns River, and no large adults (>10 pounds) have been sighted in this area (FWRI 2007 e )

. Due to the limited catch of shortnose sturgeon in the vicinity of the St. Johns River, the ir occurrence within the entrance channel and the offshore areas near the alternative sites is unlikely.



### 2.3.2. Smalltooth Sawfish The historic range of smalltooth sawfi sh in the Atlantic Ocean and Gulf of Mexico was from Texas to Cape Hatteras, North Carolina, with a large number of occurrences in Florida ( NAVFAC 2008 )

. This elasmobra nch species requires warm water and is rarely found north of southern Florida during winter months

. Juveniles inhabit exclusively nearshore habitats such as mangroves, river mouths, and coastal bay waters, while adults populate similar nearshore habitats in addition to offshore waters

. Smalltooth sawfish was listed as endangered in 2003 (NMFS 2003b)

. The loss and degradation of juvenile and adult habitat and the concurrent high incidence of fisheries bycatch for adults are the likely causes of decline

. Current distribution is reduced by as much as 95%, with regular occurrences of the species restricted to the southern tip of Florida from the Caloosahatchee River to the Florida Keys

. Smalltooth sawfish are late to mature, slow

- growing, and produce small numbers of young (NMFS 2006b ).

The area of occurrence for smalltooth sawfish includes a variety of nearshore habitats

. The action area includes nearshore habitat areas, but smalltooth sawfish have not been sighted regularly in the area, or in any area of northern Florida, since the 18 00s

. The majority of sightings in northern Florida have been large individuals, thought to be part of southern populations transiting through the area

. There has been only one confirmed sighting of this species in northern Florida during winter months

. The NMFS draft recovery plan states a need for this species to repopulate the coast of Florida, but due to its location in regards to the current southern distribution of this species, th e action area (Northern Florida) is not one of the main areas to be r epopul ated (NMFS 2006b )

. Due to its sporadic and rare occurrence anywhere north of southern Florida, it is considered very unlikely that small tooth sawfish would occur within the project area.



### 2.3.3. Atlantic Sturgeon The Atlantic sturgeon is included because this species is proposed to be listed as endangered during the course of this EIS / National Environmental Policy Act ( NEPA ) process

. Federal agencies and the public are encouraged to consider this species during project planning

. The historic range of the Atlantic sturgeon is from St. Croix, Maine, to the St. Johns River, Florida

. They spend most of their lives in marine waters and migrate up rivers from February through March to spawn

. Threats from dredging, water quality, and commercial bycatch like ly contribute to the population decline of this species

. Due to habitat degradation, the St. Johns River is suspected to serve as only a nursery for existing Atlantic sturgeon that still utilize the waterway system (NMFS and USFWS 1998)

. The St. Johns Ri ver is not currently used for spawning

, and historic al use of the river is unknown (ASSRT 2007)

. Therefore, it is unlikely that the Atlantic sturgeon will inhabit the waters within the entrance channel and federal navigation channel

. However, because the Atlantic sturgeon spends a majority of its life in marine waters,Appendix C: Biological Assessment

16 this species may be present in the offshore areas in the vicinity of the alternative sites and in the transit areas between dredge project area s and the ODMDS ( Figure 2

- 6 ).

A large U.S. co mmercial fishery (100,000 to 250,000 lbs/year) existed for the Atlantic sturgeon f ro m the 1950s through the mid

- 1990s; the origin of the fishery dates back to colonial times (NMFS 2009)

. The Atlantic sturgeon is managed under a Fishery Management Plan implemented by the Atlantic States Marine Fisheries Commission (ASMFC) , which implemented a coast

- wide moratorium on the harvest of wild Atlantic sturgeon in late 1997/early 1998

. NMFS followed this with a similar moratorium for f ederal waters

. The statu s has been periodically reviewed since being identified as a candidate species for listing under the ESA in 1991 (NMFS 2010)

. In 2007, a Status Review Team (SRT) consisting of biologists from NMFS, U.S. Geological Survey (USGS), and USFWS completed a stat us review report on Atlantic sturgeon in the United States

. The report was reviewed and supplemented by eight state and regional experts who provided their individual expert opinions on the scientific facts contained in the report and provided additional information to ensure the report provided the best available data

. Lastly, the report was peer

- reviewed by six academic experts

. NMFS evaluated th e status review report and all other best available information to determine if listing Atlantic sturgeon

un der the ESA as either threatened or endangered was warranted

. The SRT recommended that Atlantic sturgeon in the United States be divided into the following five DPSs: Gulf of Maine; New York Bight; Chesapeake Bay; Carolina; and South Atlantic

. After rev iewing the available information on the Carolina and South Atlantic DPSs ( the two DPSs located within the NMFS Southeast Region )

, NMFS determined that listing these two DPSs as endangered was warranted

, and in October 2010 propose d to list the m as endangered under the ESA (NMFS 2010 )

. The Final Listing Rule for South Atlantic and Carolina DPSs of Atlantic sturgeon in the southeast region was published in the Federal Register on February 6, 2012 (77 FR 5914).Appendix C: Biological Assessment

17Appendix C: Biological Assessment

18 

## 3. EFFECTS OF PROPOSED ACTION

This section presents an analysis of potential direct and indirect eff ects on ESA

- listed species as a result of the p roposed a ction

. Potential activities that may affect ESA

- listed species include in

- water disturbances such as movement by surface s upport vessels and dredged material disposal operations

. Direct effects would be associated with physical encounters of surface vessels with a listed species and effects of disposed material in the water column and benthic environments

. Indirect effects typically result from ancillary activities that are influenced by disposal activities or their direct effects that occur later in time and that are reasonably certain to occur (e.g., attraction of predators due to development and human presence)

. All dire ct and indirect project effects on listed species have been further classified and evaluated based on their anticipated longevity (i.e., temporary or permanent effects)

. Table 3

- 1 provides a summary of the potential direct and indirect effects on ESA

- listed species with implementation of the p roposed a ction

.

Table 3

- 1

. Summary of the Potential Direct and Indirect Effects on ESA

- L isted Species

Direct Effects Indirect Effects Species Temporary Permanent Temporary Permanent FISH Shortnose sturgeon No No No No Atlantic sturgeon No No No No Smalltooth sawfish No No No No SEA TURTLES Loggerhead Yes No No No
Leatherback Yes No No No Kemp's r idley Yes No No No Green Yes No No No MARINE MAMMALS North Atlantic right whale Yes No No No Humpback whale Yes No No No

As they relate to the ESA

- listed species and critical habitat considered in this BA, direct and indirect effects from proposed activities within the action area have been evaluated based upon (1 ) an understanding of the methods and equipment that would be used during dredge material disposal operations, (2 ) knowledge of the potential for such methods and equipment to disturb the natural resources on which the subject species depend, and (3 ) awareness of the types of effects that have resulted fro m similar actions in the past.

The use of surface support vessels during the disposal activities to the proposed ODMDS would not significantly change the airborne or u nderwater noise environment within the action areas

. The alternative sites are currently transited regularly by numerous commercial and recreational vessels, recreational boaters

, and other surface vessels (e.g., freight ers )

. Therefore, the potential eff ects of airborne or underwater noise from surface vessels on listed species are not discussed further.Appendix C: Biological Assessment

19 

## 3.1. Sea Turtles

S ea turtles are at risk from collisions with vessels since they spend time breathing and sunning on the surface of the water. Little inform ation is available on the types of vessels responsible for turtle deaths or injury, although the focus has tended to be on recreational boat traffic (National Research Council 1990). Surface vessels would transit to and from the ODMDS to dispose of dredge d materials, and heightened vessel activity may lead to collisions between vessels and sea turtles. The dredge contractors would adopt avoidance and minimization measures to reduce the potential for collisions with sea turtles at the surface. Vessels ass ociated with the transport of dredged material to the ODMDS are expected to implement actions, where feasible, to avoid interactions with sea turtles, including maneuvering away from the animal or slowing the vessel. However, during poor sighting conditio ns (i.e.

, fog, high sea state, darkness), detecting sea turtles can be difficult and there is higher potential for a vessel strike. Nevertheless, the potential for a collision between a vessel and a sea turtle is expected to be unlikely due to the type an d nature of the proposed activities within the action area.

Disposal activities at the ODMDS can potentially reduce food availability by burying and altering the benthic habitat and creating temporary increases in turbidity. The effect of increased turbidity on sea turtles is expected to be minimal due to the short duration of the reduced water clarity. The effects of burial on benthic infauna could be persistent within the boundaries of the ODMDS since disposal operations re peatedly impact the same area, potentially making it difficult for benthic infauna to fully recover within the disposal footprint or altering species composition. However, the approximately 4

- nmi 2 ODMDS represents only a small portion of this type of bent hic habitat available in the region, and only a small portion of the ODMDS would be impacted during each disposal event. Therefore, the proposed action is not likely to adversely affect sea turtles.

Loggerhead critical habitat is located approximately 3. 4 miles to the west of the proposed ODMDS. Transiting to and from the mouth of the St. John s River to the ODMDS would not occur within critical habitat. Predominate current direction is to the north and south. Therefore any disposal plumes would not be tra nsported to the critical habitat. Designation of the expanded ODMDS would not result in the addition of any obstructions, artificial lighting or manmade objects within the critical habitat Therefore, t he primary constituent elements that support this habit at would not be affected and the proposed action would not adversely affect critical habitat.



## 3.2. Marine Mammals
The following section discusse s the potential effects of the proposed a ction on North Atlantic right whale s and humpback whales within the project area. As effects in the marine environment are similar for the two whale species in the assessment, the analysis will be combined for both species. Dredged material disposal activities and their potential effects on listed whale species are addressed. The primary concern is an increase in the level of surface vessel activity in the action area (NAVFAC 2008).

Disturbance from ships transiting through the area would not be significantly different from normal vessel operations that occur daily in the pr oject area, although during dredging activities there would be an increase in vessel activity in the area between the river entrance and the propo sed ODMDS . Impacts from disposal operations are expected to be consistent with previous findings by NMFS (NMF S 1991, 1995). Since these consultations were completed, (1) the estimated number of North Atlantic right whale s has increased based on the data presented in the NMFS annual stock assessments and the numbers of North Atlantic rightAppendix C: Biological Assessment

20 whale s reported by the New England Aquarium in their annual "Right Whale Report Card"; (2) implementation of the early warning system ( EWS ) associated with operations near or within the calving grounds has been solidified by Memorandum of Agreement and has been in place since 19 89; and (3) USACE's involvement with and awareness of North Atlantic right whale issues has increased significantly. Based on these factors, USACE expects that disposal operations will have a minimal effect on North Atlantic right whale s. There would be no permanent or indirect effects associated with the proposed action

.

Critical h abitat a nalysis of the potential effects of the p roposed a ction on North Atlantic right whale critical habitat was based on an analysis of the impacts on the habitat itself a nd those elements that make up habitat. The actual physical habitat located outside the St. Johns River channel is part of the designated North Atlantic right whale critical habitat, and no alteration to this portion of critical habitat would occur. The alternatives are located in North Atlantic right whale critical habitat, but dredged materials would settle out to the benthos, which is not considered part of the critical habitat. Dredged materials would travel through the water column and would result in localized, short

- term changes in the water column as sediments settle on the seafloor

. Because of the low

- level releases, dilution, and the transient natures of water masses, adverse effects to water quality should be local and short

- term and should ha ve minimal effect on the region (USEPA 1983). Based upon the current analysis of potential effects on designated critical habitat, implementation of the proposed a ction within the project area would not compromise the function or relevance of any habitat indicators or critical habitat elements. The proposed a ction would not increase fragmentation of the North Atlantic right whale population nor decrease the function of any calving areas. Therefore, imple mentation of the p roposed a ction would not destroy or adversely modify North Atlantic right whale critical habitat.



## 3.3. Fish

3.3.1. Shortnose and Atlantic Sturgeon FWRI concluded that with the lack of current sightings in surveys, the patchy and ext remely infrequent catch of small individuals, and the historic low numbers, it is highly unlikely that significant population s of shortnose or Atlantic sturgeon currently reside within the St. Johns River

. The proposed ODMDS will be located several miles offshore the mouth of the St. Johns River , and though some individuals may be present in the marine waters in the area of alternative sites

, shortnose and Atlantic sturgeon are not likely to be adversely affected by the proposed a ction

.



### 3.3.2. Smalltooth Sawfish

Encounter data indicate that smalltooth sawfish can be found with some regularity only in south Florida from Charlotte Harbor to Florida Bay

. A limited number of reported encounters (one each in Georgia, Alabama, Louisiana, and Texas) have occurred outsi de of Florida since 1998

. Peninsular Florida is the main U.S. region that historically and currently hosts the species year

round because the region provides the appropriate climate (subtropical to tropical) and contains the habitat types (lagoons, bays, mangroves, and nearshore reefs) suitable for the species

. Encounter data and research efforts indicate that a resident, reproducing population of smalltooth sawfish exists only in southwest Florida (Simpfendorfer and Wiley 2005)

.

Smalltooth sawfish have not been sighted in the action area

. The closest sawfish encounter documented in Mote Marine Laboratory’s Sawfish Encounter Database (1999

- 2006) was near St. Augustine in the Atlantic Ocean (Simp f endorfer and Wiley 2006)

. In the unlikely event a sawfish is presen t in the project area, sawfish should not be affected by the vessels transiting toAppendix C: Biological Assessment

21 the ODMDS because they advance at a slow pace and are noisy ; giving mobile sawfish the opportunity to get out of the way (no sawfish take by a dredge has ever been reported to NMFS)

. Additionally, prey items (e.g., fish and crustaceans) are not limiting in Florida’s east coast waters and, since mangroves are not affected, it is unlikely that foraging habitats for smalltooth sawfish will be affected

. Therefore, smalltooth sa wfish are not likely to be adversely affected by the p roposed a ction

.Appendix C: Biological Assessment

22 This page intentionally left blank.Appendix C: Biological Assessment

23 

## 4. MEASURES TO AVOID, M INIMIZE, AND COMPENS ATE FOR EFFECTS

4.1. Sea Turtles
USACE will comply with applicable win dows and protective measures for protection of sea turtles as stated in the most current South Atlantic Regional Biological Opinion (SARBO). NMFS and USFWS will be consulted on specific dredging projects

, and separate b iological

o pinions may be prepared f or those projects. USACE will comply with any special conditions associated with those project

- specific b iological o pinions.

In general, to minimize the potential for collisions, vessels transporting dredged materials to the ODMDS are expected to impleme nt protective measures, where feasible, to avoid interactions with sea turtles, including maneuvering away from the animal or slowing the vessel, particularly during poor sighting conditions (i.e., fog, high sea state, darkness). During transport of dredg ed material to the ODMDS and when returning to the dredging site, vessels would use caution and proceed at a speed such that the vessel can safely take proper and effective action to avoid a potential collision with a sea turtle; this preventative action w ould significantly reduce the potential for a vessel strike with a sea turtle. Any collision with and/or injury to a sea turtle shall be reported immediately to the NMFS’s Protected Resources Division and the local authorized sea turtle stranding/rescue o rganization.

Despite these precautions, turtles may prove very difficult to spot from a moving vessel when they are resting below the water surface, during nighttime, and during periods of inclement weather. It is assumed, however, that a collision betwe en a sea turtle and moving vessel is unlikely. Adult, subadult, and perhaps juvenile turtles are capable of avoiding moving dredge

related vessels, especially when the vessels operate within these limited areas at slow to relatively slow speeds. Impacts from collisions are, consequently, not likely to adversely affect marine turtle populations within the project area.



## 4.2. Marine Mammals
To minimize project impacts on right whales and other marine mammals related to transporting dredged material to the new ODMDS, USACE will comply with the terms and conditions of the most recent SARBO. As with the sea turtles, NMFS and USFWS will be consu lted on specific dredging projects

, and separate b iological o pinions may be prepared for those projects. USACE will comply with any special conditions associated with those project

- specific b iological

o pinions.Appendix C: Biological Assessment

24 This page intentionally left blank.Appendix C: Biological Assessment

25 

## 5. CUMULATIVE EFFECTS A NALYSIS

The Council on Environmental Quality's (CEQ) regulations (40 CFR §§ 1500

- 1508) implementing the procedural provisions of the NEPA of 1969, as amended (42 U.S.C. §§ 4321 et seq.), define cumulative effects as

The impact on the environment which results from the incremental impact of the action when added to other past, present, and reasonably foreseeable future actions regardless of what agency (Federal or non

- Federal) or person undertakes such other actions (4 0 CFR § 1508.7).

Similar and unrelated actions occurring in the vicinity of the action area includ e navigation channel maintenance, commercial and recreational fishing, sand borrow areas, and shipping traffic

. Past projects include the designation of the existing Jacksonville ODMDS and Fernandina Beach ODMDS, including their ongoing use

. Ongoing projects include the maintenance of the Jackson ville Harbor Federal Navigation entrance channel and the Naval Station Mayport entrance channel and turning basin

. Recently completed projects include the Naval Station Mayport deepening. Reasonably foreseeable future actions include the Jacksonville Harbor Deepening project and the designation an d use of s and b orrow a reas

. The designation of an expanded or new ODMDS is not expected to introduce new human activities in the project vicinity

. Commercial shipping and recreational and commercial fishing are expected to continue

. Increased vessel traffic associated with the implementation of the Naval Station Maypor t and Jacksonville Harbor Deepening Projects may lead to an increased risk of animal collisions with vessels transiting to and from the ODMDS during initial construction ; however, observance of critical habitat designation s and the North Atlantic right whale EWS would mitigate for this potential increase

. The increased vessel traffic associated with these projects may also affect water quality at a greater frequency than existing circumstances

. These effects are expected to be temporary.Appendix C: Biological Assessment

26 This page intentionally left blank.Appendix C: Biological Assessment

27 

## 6. CONCLUSION

Table 6

- 1 summarizes the determination of effects on listed species and critical habitat as presented in the previous sections from implementation of the p roposed a ction

.

Table 6

- 1

. Summary of Effects on Listed Species and Critical Habitat

Species ESA Status Effects Determination
FISH Shortnose sturgeon Endangered N ot likely to adversely affect Atlantic sturgeon Endangered N ot likely to adversely affect
Smalltooth sawfish Endangered N ot likely to adversely affect

SEA TURTLES Loggerhead Threatened * May affect, not likely to adversely affect

Leatherback Endangered May affect, not likely to adversely affect Kemp's Ridley Endangered May affect, not likely to adversely affect

Green Endangered May affect, not likely to adversely affect

MARINE MAMMALS North Atlantic right whale Endangered * May affect, not likely to adversely affect Humpback whale Endangered May affect, not likely to adversely affect

* Critical habitat designated in the area of the Proposed ActionAppendix C: Biological Assessment

28 This page intentionally left blank.Appendix C: Biological Assessment

29 

## 7. LITERATURE CITED

ANAMAR. 2010. Final Report and Addendum to Final Report

– Jacksonville ODMDS Reconnaissance Sidescan Sonar Survey. Submitted to U.S. Army Corps of Engineers, Jacksonville District , Jacksonville, Florida. August 2010.

Atlantic Sturgeon Status Review Team ( ASSRT )

. 2007

. Status Review of Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus )

. Report to National Marine Fisheries Service.

Conley, W.J. and B.A. Hoffman. 1987. Nesting Activity of Sea Turtles in Florida, 1979

- 1985. Florida Scientist 50:201

- 210.

DoN (Department of the Navy). 2002. Marine Resource Assessment for the Charleston/Jacksonville Operating Area. Final Report. Naval Facilities Engineering Command, Norfolk, VA. August.

DoN. 2007a. Final Integrated Natural Resources Management Plan for Naval Station Mayport, Mayport, Florida. October.

DoN. 2007b. Notice of Intent to Prepare an Environmental Impact Statement/Overseas Environmental Impact Statement for Navy Atlantic Fleet Training in the Navy Cherry Point Range Complex and Notice of Public Scoping Meetings. Federal Register 72:21248

- 21249.

DoN. 2007c. Notice of Intent to Prepare an Environmental I mpact Statement/Overseas Environmental Impact Statement for Navy Atlantic Fleet Training in the Jacksonville Range Complex and Notice of Public Scoping Meetings. Federal Register 72:3806

- 3807.

DoN. 2008. Marine Resources Assessment Update for the Charl eston/Jacksonville Operation Area Final Report

.
Eckert, K.L

. 1995

. Leatherback Sea Turt le, Dermochelys coriacea

. National Marine Fisheries Service and FWS status reviews for sea turtles listed under ESA 1973

. P.T. Plotkin, editor

. NMFS, Silver Sprin g, MD.

Eckert, S.A. and K.L. Eckert, P. Ponganis, and G.L. Kooyman

. 1989

. Diving and Foraging Behavi or of Leatherback Sea Turtles ( Dermochelys coriacea )

. Canadian Journal of Zoology 67:2834

- 2840.

FWRI (Florida Wildlife Research Institute)

. 2007a

. Statewide Nesting Beach Survey Program Loggerhead (Caretta caretta) Nesting Data, 1990

- 2006

. http://myfwc.com/research/wildlife/sea

- turtles/nesting/beach

- survey

- totals/

FWRI

. 2007b

. Reported Nesting Activity of the Kemp’s Ridley, Lepidochelys kempii , i n Florida, 1979

- 2006; Data Summary Date: 11 May 2007

.

FWRI

. 2007c

. Statewide Nesting Beach Survey Program Green Turtle ( Chelonia mydas ) Nesting Data, 1990

- 2006

.Appendix C: Biological Assessment

30 FWRI

. 2007d

. Statewide Nesting Beach Survey Program Leatherback ( Dermochelys coriace a ) Nesting Data, 1990

- 2006.

FWRI

. 2007e

. Shortnose Sturgeon Population Evaluation in the St. Johns River, Florida

. http://myfwc.com/research/saltwater/sturgeon/research/population

- evaluation/

FWRI

. 2009

. Right Whales Research Ac tivities

. http://research.myfwc.com/images/articles/18051/r_right_whales.pdf

FWRI

. 201 1

. Sea turtle nesting data retrieved from http://myfwc.com/research/wildlife/sea

turtles/nesting/statewide/

. A ccessed 2/27/12.

Jensen, A.S. and G.K. Silber

. 2004

. NMFS Large Whale Ship Strike Database

. NOAA Technical Memorandum NMFS

- OPR

- 25

. January.

NARWC ( North Atlantic Right Whale Consortium ) . 2007. North Atlantic Right Whale Consortium Sightings Database. New England Aquarium, Boston, MA. 31 July.

NARWC . 2011

. North Atlantic Right Whale Annual Report Card, November 201 1 [online publication]. Accessed 0 2 /2 7 /1 2.

National Research Council

. 1990

. Decline of the Sea Turtles: Causes and Prevention

. National Academy Press, Washington, DC.

NAVFAC . 2008. Final Environmental Impact Statement for the Proposed Homeporting of Additional Surface Ships at Naval Station Mayport, Florida

. November 2008.

NMFS (National Marine Fisheries Service)

. 1978

. Listing and Protecting Loggerhead Sea Turtles as “Threatened Species” and Populations of Green and Olive Ridley Sea Turtles as Threatened Species or “Endangered S pecies”

. Federal Register 43:32800

- 32811.

NMFS

. 1991

. Recovery Plan for the Humpback Whale ( Megaptera novaeangliae )

. Silver Spring, Maryland: National Marine Fisheries Service.

NMFS

. 1994

. Critical Habitat for Northern Right Wh ale ( Eubalaena glacialis )

. Federal Register 59:28805

- 28835.

NMFS

. 1995

. Regional Biological Opinion for Hopper Dredging of Channels and Beach Nourishment Activities in the Southeastern United States from North Carolina through Florida East Coast

. Office of Protected Resources, Silver Spring, MD and Southeast Regional Office, Jacksonville, FL

. 25 August.

NMFS

. 1998

. Final Recovery Plan for the Shortnose Sturgeon ( Acipenser brevirostrum )

. Prepared by the Shortnose Sturgeon Recovery Team for NMFS, Silver Spring, MD

. December.

NMFS

. 2003b

. Endangered and Threatened Species; Final Endangered Status for a Distinct Population Segment of Smalltooth Sawfish ( Pristis pectinata ) in the United States

. Federal Register 68:15674

- 15680.Appendix C: Biological Assessment

31 NMFS

. 2004

. Recovery Plan for the North Atlantic Right Whale ( Eubalaena glacialis )

. Silver Spring, MD

. August.

NMFS

. 2006a Review of the Status of the Right Whales in the North Atlantic and North Pacific Oceans

. Silver Spring, MD

. December.

NMFS

. 2006b

. Draft Recovery Plan for Sm alltooth Sawfish ( Pristis pectinata )

. Prepared by the Smalltooth Sawfish Recovery Team for NMFS, Silver Spring, MD

. August.

NMFS

. 2007b

. National Marine Mammal Health and Stranding Response Database and the Southeast Region Marine Mammal Stranding Dat abase for Duval, Nassau, and St. Johns Counties , Florida (1991

- 2006)

. Southeast Marine Mammal Stranding Network.

NMFS. 2010a. Species under the Endangered Species Act ( ESA ) http://www.nmfs.noaa.gov/pr/species/esa/

NMFS. 2010b. Endangered and Threatened Wildlife and Plants; Proposed Listings for Two Distinct Population Segments of Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus ) in the Southeast. 50 CFR Part 224. NOAA.

NMFS

. 2010 c

. 50 CFR Part 224, Federal Register/Vol. 75, No. 193/Wednesday, October 6, 2010/Proposed Rules

.

NMFS and USFWS (National Marine Fisheries Service and U.S. Fish and Wildlife Service)

. 1992a

. Recovery Plan for Kemp’s Ridley Sea Turtle ( Lepidochelys kempii )

. Prepared by the Kemp’s Ridley Recovery Team for USFWS, Southwest Region, Albuquerque, NM and NMFS, Washington, DC.

NMFS and USFWS

. 1992b

. Recovery Plan for Leatherback Turtles Dermochelys coriacea in the U.S

. Caribbean, Atlantic, and Gulf of Mexico. NMFS, Washington, DC.

NMFS and USFWS

. 1993

. Recovery Plan U.S. Population of Loggerhead Turtle Caretta caretta

. Prepared by the Loggerhead/Green Turtle Recovery Team for USFWS, Southeast Region, Atlanta, GA and NMFS, Washington, DC

.

NMFS and USFWS

. 1998

. Status Review of the Atlantic Sturgeon

. National Marine Fisheries Service and United States Fish and Wil dlife Service, Washington, D.C.

NMFS and USFWS. 2007a. Loggerhead Sea Turtle ( Caretta caretta) , 5

- year Review: Summary a nd Evaluation. NMFS, Silver Spring, MD and USFWS, Jacksonville, FL. August.

NMFS and USFWS

. 2007 b

. Kemp’s Ridley Sea Turtle ( Lepidochelys kempii ), 5

- Year Review: Summary and Evaluation

. NMFS, Silver Spring, MD and USFWS, Jacksonville, FL

. August.

NMFS and USFWS

. 2007 c

. Green Sea Turtle ( Chelonia mydas ), 5

- Year Rev iew: Summary and Evaluation

. NMFS, Silver Spring, MD and USFWS, Jacksonville, FL

. August.

Simpfendorfer, Colin A

. and Tonya R. Wiley

. 2005

. Final Report : National Smalltooth Sawf ish Encounter Database

. Center for Shark Research, Mote Marine Laboratory, Sarasota, FL.Appendix C: Biological Assessment

32 Simpfendorfer, Colin A. and Tonya R. Wiley

. 2006

. Final Report : National Smalltooth Sawfish Encounter Data base

. Center for Shark Research, Mote Marine Laboratory, Sarasota, FL.

USACE (U.S. Army Corps of Engineers)

. 2008a

. USACE Sea Turtle Data Warehouse: Data on Kemp’s Ridley Sea Turtle Takes

. http://el.erdc.us ace.army.mil/seaturtles/species.cfm?Species=LK&Type=District&Code=SAJ

.

USACE

. 2008b

. USACE Sea Turtle Data Warehouse: Data on Green Sea Turtle Takes

. http://el.erdc.usace.army.mil/seaturtles/species.cfm?Species=CM&Type=District&Code=SAJ

. USEPA ( U.S. Enviro nmental Protection Agency ). 1983. Final Environmental Impact Statement for Jack sonville Harbor, Florida, Ocean Dredged Material Disposal Site Designation. USEPA Criteria and Standards Division. Washington, D.C.

Zani, M.A., A.R. Knowlton, S.D. Kraus, K.M. Lagueux, and H.M. Pettis

. 2006

. Aerial Surveys to Reduce Ship/Whale Collisi ons in the Calving Ground of the North Atlantic Right Whale ( Eubalaena glacialis )

. Annual r eport submitted to NOAA.

Zani, M.A., A.R. Knowlton, K.M. Lagueux, P. Hamilton, S.D. Kraus, and H.M. Pettis

. 2008

. Aerial Surveys to Reduce Ship/Whale Collisions in the Calving Ground of the North Atlantic Right Whale (Eubalaena glacialis)

. Annual Report submitted to NOAA.Appendix C: Biological Assessment

33 

## 8. LIST OF PREPARERS

This Biological Assessment was prepared by ANAMAR Environmental Consulting, Inc. for the U.S. Army Corps of Engi neers

– Jacksonville District.

USACE Project Manager
Patrick Griffin USACE

- Jacksonville District 701 San Marco Blvd. Jacksonville, Florida 32207

ANAMAR Environmental Consulting, Inc.

Lead Technical Writer : Christine Smith Technical Editor and Project Manager: Michelle Rau ANAMAR Environmental Consulting, Inc 2106 NW 67 th Place Suite 5 Gainesville, Florida 32653