U. S. Army Corps of Engineers, Mobile District




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U.S. Army Corps of Engineers, Mobile District

Planning and Environmental Division

Environmental Resources Branch

Coastal Environment Team


October 2011


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TABLE OF CONTENTS



  1. Introduction……………………………………………………………………………. 1

1.1 Threatened and Endangered Species and/or Designated Critical Habitat………1


  1. Description of the Proposed Action……………………………………………………. 4

    1. Gulfport Harbor, MS…………………………………………………………… 5

    2. Biloxi Harbor, MS………………………………………………………………6

    3. Pascagoula Harbor, MS…………………………………………………………8

    4. Jourdan & Wolf Rivers and Bayou Portage, MS………………………………. 10

    5. Bayou Caddy, MS……………………………………………………………… 12

    6. Pass Christian, MS………………………………………………………………13

    7. Gulf Intracoastal Waterway (GIWW), MS…………………………………….. 13

    8. Bayou La Batre, AL……………………………………………………………. 14

    9. Bayou Coden, AL……………………………………………………………… 15

2.10 Dog River, AL…………………………………………………....………....... 15

2.11 Fowl River, AL…………………………………………………………….…. 16

2.12 Mobile Harbor, AL………………………………………….…………........... 17

2.13 Fly Creek, AL…………………………………………………………….…... 20

2.14 Bon Secour, AL…………………………………………………………….… 21

2.15 Perdido Pass, AL……….……………………………………………………... 21

2.16 Gulf Intracoastal Waterway (GIWW), AL…………………………………… 23

2.17 East Pass, FL………………………………………………………………….. 24

2.18 Pensacola Harbor, FL…………………………………………………………. 25

2.19 Panama City Harbor, FL……………………………………………………… 27

2.20 Gulf Intracoastal Waterway (GIWW), FL……………………………………. 28

2.21 St. George Island (Sike’s Cut), FL……………………………………………. 29

2.22 Scipio Creek, FL……………………………………………………………… 30

2.23 East Point, FL………………………………………………………………… 30

2.24 Carrabelle Harbor, FL………………………………………………………… 31

2.25 Escambia River, FL……………………………………………………………31


  1. Action Area…………………………………………………………………………...... 33

3.1 Projects Excluded From Further Analysis……………………………………. 35

3.1.1 Pascagoula Harbor, MS………………………………………………...... 35

3.1.2 Jourdan & Wolfe Rivers and Bayou Portage, MS……………………….. 35

3.1.3 Pass Christian, MS……………………………………………………….. 35

3.1.4 GIWW, MS………………………………………………………………. 35

3.1.5 Pensacola Harbor, FL…………………………………………………….. 35

3.1.6 GIWW, FL……………………………………………………………….. 35

3.1.7 Scipio Creek, FL…………………………………………………………. 35

3.1.8 Carrabelle Harbor, FL……………………………………………………. 36

3.1.9 Escambia River, FL……………………………………………………… 36

3.1.10 Alabama Projects Excluded from Further Analysis……………………. 36


  1. Conservation Measures………………………………………………………………… 36




  1. Species Accounts and Status of the Species in the Action Area……………………….. 36

    1. Distribution of Status…………………………………………………………... 37

    2. Feeding Habits………………………………………………………………..... 37

    3. Reproduction…………………………………………………………………… 38

    4. Freshwater Habitat……………………………………………………………... 39

    5. Estuarine and Marine Habitat………………………………………………….. 40

    6. Migration……………………………………………………………………….. 41




  1. Critical Habitat Units…………………………………………………………………... 43

    1. Gulf Sturgeon Critical Habitat…………………………………………………. 43

    2. Unit 6 Apalachicola River……………………………………………………....43

    3. Unit 8 Lake Pontchartrain……………………………………………………… 44

    4. Unit 9 Pensacola Bay……………………………………………………..……..47

    5. Unit 10 Santa Rosa Sound……………………………………………………... 48

6.6 Unit 11 Florida Nearshore Gulf of Mexico……………………………...……... 49

6.7 Unit 12 Choctawhatchee Bay………………………………………………….. 49

6.8 Unit 13 Apalachicola Bay……………………………………………………… 51


  1. Primary Constituent Elements…………………………………………………………. 53

    1. Water Quality…………………………………………………………………... 53

    2. Riverine Spawning Area……………………………………………………….. 53

    3. Riverine Aggregation Areas…………………………………………………… 54

    4. Migratory Pathway…………………………………………………………….. 54

    5. Sediment Quality………………………………………………………………. 55

    6. Flow Regime…………………………………………………………………… 56

    7. Prey Abundance……………………………………………………………….. 56




  1. Cumulative Effects of the Proposed Action…………………………………………… 57

    1. Factors Affecting the Species’ Environment within the Action Area…………. 57

    2. Federal Actions………………………………………………………………… 57

    3. State and Local Actions………………………………………………………... 57

    4. Conservation and Recovery Actions…………………………………………… 57

    5. Cumulative Effects…………………………………………………………….. 57




  1. Conclusion……………………………………………………………………………... 58


10.0 Literature Cited……………………………………………………………………….. 59


Appendix A: List of Acronyms…………………………………………………………….. 66


Appendix B: Open Water Disposal Areas…………………………………………………. 67

Appendix C: List of Figures……………………………………………………………….. 75


BIOLOGICAL ASSESSMENT FOR OPERATION

AND MAINTENANCE OF

FEDERAL NAVIGATION PROJECTS

OF MOBILE DISTRICT IN

FLORIDA, MISSISSIPPI AND ALABAMA


September 2011


______________________________________________________________________________


  1. INTRODUCTION

The purpose of this Regional Biological Assessment (RBA) is to present U.S. Army Corps of Engineers (Corps), Mobile District, Operation and Maintenance (O&M) of Federal Navigation Projects under National Marine Fisheries Service (NMFS), Protected Resources Division’s (PRD) purview in sufficient detail to determine to what extent the associated activities may affect any of the threatened and endangered species and designated critical habitats occurring within the action area. The Corps, Mobile District, has 43 federally authorized O&M navigation projects within its jurisdiction. Not all of these projects are routinely maintained per the identified dredging cycle due to a number of reasons, such as funding constraints, reduced navigation needs and lack of disposal areas (DAs). Coordination on each individual project requires both funding and time with an already constrained budget and limited staff for the Corps and NMFS, PRD. This RBA will allow our staff to renew consultation every 10 years on Corps, Mobile District’s, O&M navigation projects, while also allowing our agencies to focus more on other projects that present greater challenges than these O&M efforts.


This initiation package is prepared in accordance with legal requirements set forth under regulations implementing Section 7 of the Endangered Species Act (ESA) (50 Federal Register (FR) 402; 16 United States Code (U.S.C.) 1536(c)). The Corps, Mobile District, requests your Section 7 concurrence with our determination that the proposed actions discussed herein are not likely to adversely affect sea turtle and Gulf sturgeon species, and are not likely to destroy or adversely modify designated critical habitat.


1.1 Threatened and Endangered Species and/or Designated Critical Habitat:


Table 1 illustrates threatened and endangered species and designated critical habitats under the jurisdiction of NMFS which may occur in or near the action area:


TABLE 1


Common Name

Scientific Name

Status

Fish







Gulf Sturgeon

Acipenser oxyrinchus desotoi

TCH

Smalltooth Sawfish

Pristis pectinata




Largetooth Sawfish

Pristis perotteti

E

Mammals







Blue Whale

Balaenoplera musculus

E

Humpback Whale

Megaptera novaeangliae

E

Fin Whale

Balaenoptera physalus

E

Sei Whale

Balaenoptera borealis

E

Sperm Whale

Physeter macrocephalus

E

West Indian Manatee

Trichechus manatus

ECH

Amphibians







Loggerhead Sea Turtle

Caretta caretta

T

Green Sea Turtle

Chelonia mydas

E

Leatherback Sea Turtle

Dermochelys coriacea

E

Kemp’s Ridley Sea Turtle

Lepidochelys kempii

E

Hawksbill Sea Turtle

Eretmochelys imbricata

E


Whales: The Corps, Mobile District, does not anticipate sperm, blue, fin, humpback, or sei whales would be adversely affected by the varying dredging methods (i.e. hydraulic, hopper, and mechanical) described in this RBA, or disposal operations along the entire proposed action area. The possibility of collision with the dredge is remote since these are deepwater species and the likelihood for collision would be enhanced by the highly mobile nature of these species. For the projects considered in this RBA which are of shallower depth, they would not provide adequate habitat for these species and they are therefore unlikely to be found in the action area. Given their likely absence, feeding habits, and very low likelihood of interaction, the Corps, Mobile District, does not anticipate the proposed aqctions identified in this RBA will affect these species. As such, sperm, blue, fin, humpback, and sei whales are not considered further in this assessment.


Sea Turtles: There are five species of sea turtles (green, hawksbill, Kemp’s ridley, leatherback and loggerhead), which may be found in or near the action area. The National Oceanic and Atmospheric Administration (NOAA) Fisheries Sea Turtle Stranding and Salvage Network records from 1998-2002 and data from 2003-2006 verify the presence of all five species along the northern Gulf of Mexico (GOM).


Proposed dredging activities would be conducted using varying dredging methods (i.e. hydraulic, hopper, and mechanical) described in this RBA. Existing Biological Opinions (BO) on hopper dredging in the U.S. South Atlantic and GOM waters (most recently, January 9, 2007, Regional Biological Opinion (RBO) to the Corps’ four GOM districts) have established that non-hopper type dredging methods have discountable effects on, or are not likely to adversely affect, currently listed sea turtles (I/SER/2006/02953; I/SER/2006/01096). In the event a hopper dredge is used for the proposed work, operational protocol strategies set forth in the 2003 Gulf RBO would be adhered to. Hydraulic dredging is not known to take sea turtles; sea turtles are highly mobile and will likely avoid the area due to project activity and noise. Normal behavior patterns of sea turtles are not likely to be significantly disrupted by the project activities because of the short-term localized nature of the activities and the ability of sea turtles to avoid the immediate area.


The project is not expected to negatively affect sea turtle foraging habitat. Leatherbacks are pelagic feeders and the modification of the benthos through the dredge and disposal activities will not affect pelagic resources. Hawksbill and green turtles are specialist feeders that target sponges and seagrass or macroalgae. The project will not adversely affect these resources. Kemp’s ridley and loggerhead sea turtles are the most likely species to occur in the action area and are generalist carnivores, typically preying on benthic mollusks and crustaceans in the nearshore environment. Both species of sea turtles can be found foraging in shallow sand-mud habitat and high-relief rock or reef habitats. The Corps, Mobile District, anticipates that any habitat and food availability effects of the project on turtles will be insignificant since the effects will be short term and the area impacted during any one dredging event is relatively small in comparison to available foraging habitat. Nesting may occur within some nearshore placement areas associated with the proposed action. After placement of dredged material along nearshore areas the Corps, Mobile District, would consult with U.S. Fish and Wildlife Service (USFWS). Considering the finding of discountable effects on sea turtles by mechanical and hydraulic dredges in the RBO and the insignificant effects to sea turtle foraging habitat these species are not considered further in this assessment.


Fishes: The United States (U.S.) population of smalltooth sawfish was listed as endangered under the ESA on April 1, 2003 (68 FR 15674); critical habitat was designated on August 27, 2009 (74 FR 45353). Historically, smalltooth sawfish commonly occurred in the shallow waters of the GOM and the Eastern Seaboard of North Carolina; current distribution is believed to be centered on the extreme southern portions of the Florida peninsula (Simpferndorfer, 2003). Records of smalltooth sawfish are rare in the action area. To the Corps, Mobile District’s knowledge there has been no observed incidental take of smalltooth sawfish by hydraulic or hopper dredges. The proposed action is not expected to have an effect on the smalltooth sawfish, given their likely absence and very low likelihood of interaction. Therefore, the species is excluded from further RBA analysis.


The U.S. population of largetooth sawfish was listed as endangered under the ESA on July 12, 2011 (76 FR 40822); critical habitat has not been designated. Historically, P. perotteti are thought to inhabit warm temperate to tropical marine waters in the eastern and western Atlantic and Caribbean. In the western Atlantic, P. perotteti occurred from the Caribbean and GOM south through Brazil, and in the United States, largetooth sawfish were reported in the GOM, mainly along the Texas coast and east into Florida waters (Burgess and Curtis, 2003; Burgess et al., 2009). Although the first confirmed record of a U.S. largetooth sawfish was from ‘‘the Gulf of Mexico’’ in 1878 (Burgess et al., 2009), they were likely present prior to this time period. Sawfish encounters were reported in the entire GOM in early popular literature of the late 1800s but the similarities between the smalltooth and largetooth sawfishes limited the ability of non-specialists to discriminate between the two species. Because of this, there is no conclusive data available for largetooth sawfish abundance before fishing and other anthropogenic pressures began to affect their distribution. Records of largetooth sawfish are rare in the action area. To the Corps, Mobile District’s knowledge there has been no observed incidental take of largetooth sawfish by hydraulic or hopper dredges. Sawfish are highly mobile and would likely avoid the area due to project activity and noise. The proposed action is not expected to have an effect on the largetooth sawfish, given their likely absence and very low likelihood of interaction. Therefore, the species is excluded from further RBA analysis.


NMFS and USFWS jointly manage Gulf sturgeon. Gulf sturgeon was listed as a threatened species on September 30, 1991 (56 FR 49653). The present range of Gulf sturgeon extends from Lake Ponchartrain and the Pearl River system in Louisiana and Mississippi east to the Suwannee River in Florida (Appendix C, Figure 1). Gulf sturgeon critical habitat was designated on March 19, 2003 (68 FR 13370) (Appendix C, Figure 2). Gulf sturgeon is an anadromous fish; adults spawn in freshwater then migrate to estuarine/marine habitats. Both adult and subadult Gulf sturgeon migrate from estuaries, bays and the GOM to the coastal rivers in early spring (i.e. March through May) when river water temperatures range from 16 to 23°C (Huff, 1975; Carr, 1983; Wooley and Crateau, 1985). Generally, fall downstream migration from the river into the estuary/GOM begins in September and continues through November.


Maintenance dredging is dependent on shoaling in the channel and therefore may occur during periods of sturgeon migration and/or wintering activities. Proposed dredging activities would be conducted using varying dredging methods (i.e. hydraulic, hopper, and mechanical) described in this RBA. Dredging conducted by hydraulic dredges is not known to take Gulf sturgeon. Existing BOs on hopper dredging in the U.S. South Atlantic and GOM waters (most recently, January 9, 2007, RBO to the Corp’s four GOM districts) have established that non-hopper type dredging methods have discountable effects on, or are not likely to adversely affect, Gulf sturgeon. In the event a hopper dredge is used for the proposed work, operational protocol strategies set forth in the 2003 Gulf RBO would be adhered to. Sturgeon are highly mobile and would likely avoid the area due to project activity and noise. Considering the finding of discountable effects on Gulf sturgeon by mechanical and hydraulic dredges in the RBO, effects on the species are not considered further in this assessment. Potential impacts to critical habitat of Gulf sturgeon are considered herein.

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