Biological Opinion on EPA approval of FL water quality standards under Sec 303 of CWA signed ...

268 Pages·2016·4.18 MB·English

NATIONAL MARINE FISHERIES SERVICE
ENDANGERED SPECIES ACT SECTION 7
BIOLOGICAL OPINION
Title: Biological Opinion on EPA Approval of Water Quality
Standards Under Section 303 of the Clean Water Act
Consultation Conducted By: Endangered Species Act Interagency Cooperation
Division, Office of Protected Resources, National
Marine Fisheries Service, National Oceanic and
Atmospheric Administration, U.S. Department of
Commerce
Action Agency: Environmental Protection Agency, Region 4, Atlanta,
Georgia
Publisher: Office of Protected Resources, National Marine Fisheries
Service, National Oceanic and Atmospheric
Administration, U.S. Department of Commerce
Consultation Tracking number: FPR-2015-9234
Digital Object Identifier (DOI): https://doi.org/10.7289/V5NP22H6
NATIONAL MARINE FISHERIES SERVICE

ENDANGERED SPECIES ACT SECTION 7 BIOLOGICAL OPINION

Action Agency: Environmental Protection Agency,
Region 4, Atlanta, Georgia
Activity Considered: Approval of Florida Numeric Nutrient Criteria for Total
Phosphorus, Total Nitrogen, and Chlorophyll-a, Dissolved
Oxygen Criteria, and Turbidity Limits under section 303(c ) of
the Clean Water Act 1
Consultation Conducted By: Endangered Species Act lnteragency Cooperation Division,
Office of Protected Resources, N atibnal Marine Fisheries
Service
Approved:
Public Consultation Tracking
System (PCTS) number: FPR-2015-9234

Biological Opinion on Florida Water Quality Standards PCTS FPR-2015-9234
Contents
1 Introduction ........................................................................................................................... 1

1.1 Background ...................................................................................................................... 2

1.2 Consultation History ........................................................................................................ 3

2 Description of the Action ...................................................................................................... 5

2.1 Biological Evaluation (BE) for Hierarchical Numeric Nutrient Criteria (NNC)

for Total Phosphorus (TP), Total Nitrogen (TN), and Chlorophyll a (Chl-a) ................. 6

2.1.1 Springs and Lakes ..................................................................................................... 7

2.1.2 Streams ...................................................................................................................... 7

2.1.3 Estuaries .................................................................................................................... 8

2.1.4 Site-Specific Alternative Standards (SSACs) ........................................................... 8

2.1.5 Impaired Waters Rule ............................................................................................... 9

2.2 BE for Dissolved Oxygen (DO) and Nutrient Related Revisions (NNC for Tidal

Peace River) ..................................................................................................................... 9

2.2.1 Florida's DO Criteria ................................................................................................. 9

2.2.2 Tidal Peace River NNC .......................................................................................... 11

2.3 Estuary NNC .................................................................................................................. 12

2.3.1 Coastal Waters ........................................................................................................ 12

2.3.2 Estuaries .................................................................................................................. 12

2.4 BE for Turbidity limits under Florida's Joint Coastal Permit (JCP) .............................. 13

2.5 The Coral Supplement .................................................................................................... 14

2.6 Action Area .................................................................................................................... 15

2.7 Interrelated and Interdependent Actions ........................................................................ 16

3 Overview of the Assessment Framework .......................................................................... 17

3.1 Applying a Risk Assessment Framework to the Assessment in this Consultation ....... 18

3.1.1 Effects Analysis ...................................................................................................... 21

3.1.2 Integration and Synthesis ........................................................................................ 25

4 Effects Analysis ................................................................................................................... 27

4.1 Problem Formulation...................................................................................................... 27

4.1.1 Stressors of the Action ............................................................................................ 27

4.1.2 Status of Species Listed as Endangered or Threatened under the

Endangered Species Act (ESA) and Designated Critical Habitats in the

Action Area and Under the Jurisdiction of the National Marine Fisheries

Service (NMFS) ..................................................................................................... 38

4.1.3 Environmental Baseline .......................................................................................... 83

4.1.4 Risk Hypotheses for Evaluating Approved Criteria and Limits ............................. 96

4.2 Exposure and Response Analysis ................................................................................. 103

4.2.1 Exposure: NNC ..................................................................................................... 104

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Biological Opinion on Florida Water Quality Standards PCTS FPR-2015-9234
4.2.2 Exposure: DO Criteria .......................................................................................... 133

4.2.3 Exposure: Turbidity Limits under Florida's JCP Activities Involving Beach

Nourishment ......................................................................................................... 143

4.2.4 Summary of the Exposure Analysis ...................................................................... 149

4.2.5 Response Analysis: Eutrophic Stressors in the Tidal Peace River ....................... 150

4.2.6 Response: Florida's Saturation-Based DO Criteria ............................................... 164

4.3 Risk Characterization ................................................................................................... 173

4.3.1 Risk Characterization for the Tidal Peace River NNC ......................................... 173

4.3.2 Risk Characterization for Florida's DO Criteria ................................................... 178

5 Cumulative Effects ............................................................................................................ 179

6 Integration and Synthesis ................................................................................................. 181

6.1 Integration and Synthesis of Effects of the Tidal Peace NNC on Smalltooth

Sawfish ......................................................................................................................... 181

6.2 Integration and Synthesis of Effects of the Tidal Peace NNC on Smalltooth

Sawfish Designated Critical Habitat ............................................................................ 183

6.3 Integration and Synthesis of Effects of the DO Criteria on Atlantic and

Shortnose Sturgeon ...................................................................................................... 185

7 Conclusion ......................................................................................................................... 186

8 ITS ...................................................................................................................................... 186

8.1 Amount or Extent of Take ............................................................................................ 187

8.2 Effects of the Take ....................................................................................................... 190

8.3 RPMs ............................................................................................................................ 191

8.4 Terms and Conditions .................................................................................................. 191

8.5 Conservation Recommendations .................................................................................. 193

Section 7(a)(1) of the ESA directs Federal agencies to use their authorities to further

the purposes of the ESA by carrying out conservation programs for the benefit

of the threatened and endangered species. Conservation recommendations are

discretionary agency activities to minimize or avoid adverse effects of a

proposed action on ESA-listed species or designated critical habitat, to help

implement recovery plans or develop information (50 CFR 402.02). ......................... 193

9 Reinitiation of Consultation ............................................................................................. 193

10 References .......................................................................................................................... 195

Appendix A: Summary of the Clean Water Act (CWA) ....................................................... 245

The Use of EPA Water Quality Guidelines in this Opinion ................................................... 246

National Pollution Discharge Elimination System (NPDES) ................................................. 247

Water Quality Standards ......................................................................................................... 249

Appendix B: Florida's Estuary NNC ...................................................................................... 252

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Biological Opinion on Florida Water Quality Standards PCTS FPR-2015-9234
National Estuary Program Reference Period-Based NNC Not to be Exceeded More

than Once in Three Years ............................................................................................ 252

South Florida Marine Systems NNC Based on the "Maintain Healthy Conditions

Approach" .................................................................................................................... 253

Estuary NNC Based On Reference Conditions ...................................................................... 254

Empirical Approach for the Fluctuating Influence of Freshwater Inflows ............................. 257

Estuary NNC Based on Mechanistic Modeling. ..................................................................... 257

LIST OF TABLES
Page

Table 1. Summary of Florida's Regional DO Criteria. ................................................................. 10

Table 2. Estuary Segments Excluded from the Analysis after Florida Department

of Environmental Protection Revised NNC to Higher TN, TP, and/or Chl-a
Concentrations. ............................................................................................................................. 16

Table 3. Endangered and Threatened Species and Designated Critical Habitat

Under NMFS' Jurisdiction that Occur in Florida Waters. ............................................................ 38

Table 4. Waters Listed as Impaired for Nutrients, DO, Turbidity, or Nutrient-

Related Measures. ......................................................................................................................... 93

Table 5. Nutrient-Impaired Waters with NNC Considered in this Opinion. ................................ 95

Table 6. Number of Estuary Segments with DO Impairments and Priority for

Developing Total Maximum Daily Loads (TMDLs) to Restore Designated Use. ....................... 96

Table 7. No Effect and May Effect () Determinations for EPA-approved NNC,

DO Criteria and Turbidity Limit Risk Assessment Hypotheses for ESA-listed

Species Under NMFS Jurisdiction. ............................................................................................. 100

Table 8. No Effect and May Effect Determinations for the Risk Hypothesis:

“Florida's NNC, DO Criteria, and Turbidity Limits Approved by EPA Support

Conditions that Adversely Affect the Critical Habitat, Including the Features that

are Essential to the Conservation of the Species." ...................................................................... 102

Table 9. Number of Sampling Events Reporting Chl-a Levels Within and Above

Chl-a NNC Relative to Events Reporting TP and TN Levels Within and Above

TP and TN NNC. ........................................................................................................................ 111

Table 10. Pre- and Post-TMDL, Chl-a NNC Exceedance Frequency and Ratio to

Criteriona. .................................................................................................................................... 121

Table 11. No Effect, Not likely to Adversely Affect, and May Effect ()

Determinations Resulting from the Exposure Analysis for the NNC. ........................................ 132

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Biological Opinion on Florida Water Quality Standards PCTS FPR-2015-9234
Table 12. Summary of Florida's Regional DO Criteria. ............................................................. 135

Table 13. Observed DO Concentrations in Sampling Events from Waters Not

Impaired by DO Excursions or Excess Nutrients and Meeting Oxygen Saturation

Levels within Florida’s DO Criteria. .......................................................................................... 137

Table 14. Summary of Daily Average DO Observations Among Florida Coastal

and Estuarine Waters Meeting at Least 42 percent Saturation (2007-2015). ............................. 140

Table 15. Summary of daily average DO observations among Florida coastal and

estuarine waters within designated critical habitat for ESA-listed species under

NMFS' jurisdiction and meeting at least 42 percent saturation (2007-2015). ............................ 141

Table 16. No Effect and May Effect () Determinations Resulting from the

Exposure Analysis for DO Criteria for ESA-listed Species and, Where

Designated, Critical Habitat. ....................................................................................................... 143

Table 17. Determination for the Effects of Florida's Turbidity Limits on ESA-

listed Species, and Where Designated, Critical Habitat, Based on Exposure

Analysis....................................................................................................................................... 149

LIST OF FIGURES
Page
Figure 1. Relationship Between DO Concentration and Water Temperature for

Florida's DO Criteria (from Technical Support Document, Figure 35). ....................................... 11

Figure 2. Extent of EPA's Action Area for the Approval of Florida Water Quality

Standards. ...................................................................................................................................... 15

Figure 3. Process Diagram for the Ecological Risk Assessment – Endangered

Species Act Effects Analysis Framework and Integration and Synthesis Used in

this Opinion (adapted from USEPA 1998, USFWS and NMFS, 1998). ...................................... 20

Figure 4. Direct and Indirect Effects of Stressors Due to the Interdependence of

Species. ......................................................................................................................................... 28

Figure 5. Direct and Indirect Effects of Excess Nutrients on Biological Responses. ................... 32

Figure 6. Direct and Indirect Effects of Adverse DO Conditions on Biological

Responses. ..................................................................................................................................... 34

Figure 7. Direct and Indirect Effects of Adverse Turbidity Conditions on

Biological Responses. ................................................................................................................... 37

Figure 8. North Atlantic Right Whale Designated Critical Habitat along Georgia

and Northeastern Florida Coasts. .................................................................................................. 41

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Biological Opinion on Florida Water Quality Standards PCTS FPR-2015-9234
Figure 9. Loggerhead Sea Turtle Designated Critical Habitat in Florida. .................................... 54

Figure 10. Smalltooth Sawfish Encounter Data Within Florida Waters from the
International Sawfish Encounter Database (ISED). ...................................................................... 56
Figure 11: Smalltooth Sawfish Designated Critical Habitat. ........................................................ 58

Figure 12: Florida Priority Watershed Areas Known or Having Potential to Harbor
Atlantic Sturgeon. ......................................................................................................................... 63
Figure 13. Acropora Designated Critical Habitat in Florida. ....................................................... 72

Figure 14. Johnson's Seagrass Designated Critical Habitat. a) North of Sebastian
Inlet Channel, b) South of Sebastian Inlet channel, c) Ft. Pierce Inlet, d) north of
St. Lucie Inlet, e) Hobe Sound, f) South Side of Jupiter Inlet, g) a Portion of Lake
Worth Lagoon North of Bingham Island, h) a Portion of Lake Worth Lagoon,
Located Just North of Boynton Inlet, i) a Portion of Northeast Lake Wyman, Boca
Raton, j) a Portion of Northern Biscayne Bay. ............................................................................. 82
Figure 15: Map of Major Surface Waters in Florida. ................................................................... 86

Figure 16. Concentration-based NNC for TP, TN, and Chl-a Among Estuaries.
Reference Periods, "Healthy Cond." = inclusive "Maintain Healthy Conditions
Approach," Reference Condition = excluding non-reference data for reference
sites or periods, Mech. Models = Mechanistic hydrodynamic and nutrient loading
modeling. .................................................................................................................................... 109
Figure 17. Relationship Between Chl-a and Nutrients Concentrations for the NNC
and Data from 2010-2015. The Tidal Peace River NNC are 1.08 mg/L for TN, 0.5
mg/L for TP, and 12.6 for Chl-a. Panel A Includes Sampling Events from Tidal
Peace River (Blue Symbols), Panel B Plots the Same Data Without Tidal Peace
River. The regression plane was calculated from the NNC (green symbols). ............................ 112
Figure 18. Comparison of Seagrass Coverage for Tidal Peace River and Myakka
Rivers. Red box denotes reference period. Adapted from Janicki Environmental,
2011............................................................................................................................................. 114
Figure 19. Tidal Peace River and Tidal Myakka River TN and TP Loads. Adapted
from Janicki Environmental, 2011. ............................................................................................. 114
Figure 20. Ratios of TN, TP, and Chl-a Observations Relative to NNC for Tidal
Peace River and Tidal Myakka River. ........................................................................................ 115
Figure 21. Available Data for Charlotte Harbor Estuary Segments Showing
Positive Seagrass Trends within Reference Period Used to Derive NNC. Adapted
from Janicki Environmental, 2011. ............................................................................................. 116
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Biological Opinion on Florida Water Quality Standards PCTS FPR-2015-9234
Figure 22. Distribution of TN, TP and Chl-a Data from Estuary Sampling Stations
Before and After TMDL Implementation. .................................................................................. 120
Figure 23. Pre and Post-TMDL Chl-a Levels in Relation to Kjeldahl Nitrogen and
Phosphate Levels. ....................................................................................................................... 122
Figure 24. Distribution of Florida Coastal Chl-a NNC. ............................................................. 123

Figure 25. Station and Coastal Segments Used in Remote Sensing Chl-a Analysis
and Light Attenuation for the Development of NNC. A) Florida Panhandle, West
Florida Shelf, and Atlantic Coast. B) Chl-a Estimates Versus Field-measured Chl­
a from Stations within Three Nautical Miles from the Coast (1) and for all the
Stations (2). (Gray dashed line is 1:1 fit and black line is the regression slope). ....................... 125
Figure 26. Karenia brevis Detected in Charlotte Harbor Estuary Between 2007
and 2014. ..................................................................................................................................... 131
Figure 27. Relationship Between Dissolved Oxygen Concentration and Water
Temperature for Florida Dissolved Oxygen Criteria (from Technical Support
Document, Figure 35). ................................................................................................................ 136
Figure 28. Scatterplots for Dissolved Oxygen (panels A and B) and Percent
Saturation (Panels C and D) from Continuous Monitoring Observations for U.S.
Geological Survey Stations in St. Johns and St. Marys Rivers Showing Observed
DO Concentration and Saturation Levels (Blue) and Concentration and Saturation
Levels under the DO Criteria (Red). ........................................................................................... 138
Figure 29. Subset of U.S. Geological Survey Continuous Monitoring Data for
Stations in St. Johns River and St. Marys River Showing the Time of Year and
Duration Of Periods of DO Excursions Below 5 mg/L (Panels A and B) and the
Severity of the DO Excursions Below 5 mg/L (Panels C And D). ............................................. 139
Figure 30. Active and Planned JCP Activities (FDEP 2016). .................................................... 146

Figure 31. Charlotte Harbor Detail of Smalltooth Sawfish Designated Critical
Habitat and Reported Encounters Between 2010 and 2015 (Poulakis 2016). ............................ 151
Figure 32. Effect of Time of Day on Chl-a Data in Tidal Peace River Sampling
Events with TP and TN Consistent with NNC. .......................................................................... 156
Figure 33. Pathways Linking Excess Phosphorus and Nitrogen to Adverse Effects
on the Survival and Fitness of Smalltooth Sawfish. ................................................................... 175

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Biological Opinion on Florida Water Quality Standards PCTS FPR-2015-9234
ACRONYMS AND ABBREVIATIONS
BE – Biological Evaluation RPM – Reasonable and Prudent Measure
CCC – Chronic Criterion Concentration SAB – Science Advisory Board
Chl–a – Chlorophyll a
SCI – Stream Condition Index
CMC – Criterion Maximum Concentration
SSAC – Site Specific Alternative Criteria
CWA – Clean Water Act
STORET – STOrage and RETrieval database
DO – Dissolved Oxygen
TAN – Total Ammonia Nitrogen
DPS – Distinct Population Segment
TL – Total Length
ECOTOX – ECOTOXicology database
TMDL – Total Maximum Daily Load
EPA – Environmental Protection Agency
TN – Total Nitrogen
ESA – Endangered Species Act
TP – Total Phosphorus
FAV – Final Acute Value
TSS – Total Suspended Solids
FDEP – Florida Department of Environmental
USACE – U.S. Army Corps of Engineers
Protection
USFWS – U.S. Fish and Wildlife Service
FP – Fibropapillomatosis
WQC – Water Quality Criteria
FFWCC – Fish and Wildlife Conservation
WQS – Water Quality Standard
Commission
HABs – Harmful Algal Blooms
ICWW – Intracoastal Waterway
IPCC – Intergovernmental Panel on Climate
Change
ISED – International Sawfish Encounter
Database
ITS – Incidental Take Statement
JCP – Joint Coastal Permit
LC50 – Concentration at which 50 percent of
exposed organisms die
LOEC – Lowest Observed Effect
Concentration
NH – Unionized ammonia
3
NH + – Ionized Ammonia
4
NLAA – Not Likely to Adversely Affect
NMFS – National Marine Fisheries Service
NNC – Numeric Nutrient Criteria
NOAA – National Oceanic and Atmospheric
Administration
NOEC – No Observed Effect Concentration
NPDES – National Pollutant Discharge
Elimination System
PCBs – Polychlorinated Biphenyls
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