Form for Compliance with E.O. 12866 Docket Requirements

Title of Regulation: Water Quality Standards for the State of Florida’s Estuaries, Coastal 

Waters, and South Florida Inland Flowing Waters

 

Contact person: Erica Fleisig 

Phone number: 202-566-1057 

Was this regulation reviewed by OMB under Executive Order 12866 - Regulatory Planning 

and Review?

X Yes No 

If you checked “no”, you are done with this form. Simply place it in the docket for your 

regulation. If you checked “yes”, please fill out the remainder of the form before placing it in 

the docket. Also docket any relevant documents referenced in the form.

For regulations that are checked “Yes” above:

This regulation was reviewed by OMB under Executive Order 12866 - Regulatory Planning and 

Review. 

Attached is the draft regulation and any other documents sent to OMB for review, such as 

analyses and assessments. E.O. 12866 requires agencies to make these publicly available.

E.O. 12866 also requires agencies to identify the substantive changes between the draft 

regulation sent to OMB for review and the regulation subsequently announced [Please check the 

appropriate box below:] 

 X EPA made substantive changes to this regulation

(includes changes initiated by EPA or OMB). 

Attached is a document which: (1) identifies all the substantive changes made, and (2) 

notes those changes OMB suggested or recommended.

 No substantive changes were made to this regulation

Therefore, no further attachments are required.

If you have questions about this regulation, please call the EPA contact person listed above.
MEMORANDUM

SUBJECT: Proposed Rule: Water Quality Standards for the State of Florida’s Estuaries, 

Coastal Waters, and South Florida Inland Flowing Waters - Executive Order 

12866 Docket Requirements Compliance

FROM: Erica Fleisig, Regulation Manager

Office of Water

TO: Docket EPA-HQ-OW-2010-0222

Overview

On February 7, 2012, the proposed rule titled: Water Quality Standards for the State of Florida’s 

Estuaries, Coastal Waters, and South Florida Inland Flowing Waters was submitted to the 

Office of Management and Budget (OMB) for review under E.O. 12866. On November 30, 

2012, OMB concluded review of the proposed rule.

This review resulted in a number of substantive changes being made to the proposed rule as a 

result of recommendations from OMB or other agencies. In addition to the in-text edits captured 

in the attached preamble, other changes were initiated by EPA or OMB in response to three 

significant events that occurred while the proposed rule was at OMB. A summary of those events 

and the resulting changes is captured below.

Background

On January 14, 2009, EPA determined under CWA section 303(c)(4)(B) that new or revised 

water quality standards (WQS) in the form of numeric nutrient water quality criteria for nitrogen 

and phosphorus pollution are necessary to protect the designated uses that Florida has set for its 

Class I, Class II, and Class III waters. Subsequently, EPA entered into a Consent Decree, 

effective on December 30, 2009 (and further revised on several occasions), which established a 

schedule for EPA to propose and promulgate numeric nutrient criteria for Florida’s lakes, 

springs, flowing waters, estuaries, and coastal waters. The Consent Decree provided that if 

Florida submitted and EPA approved numeric nutrient criteria for the relevant waterbodies 

before the dates outlined in the schedule, EPA would no longer be obligated to propose or 

promulgate criteria for those waterbodies.

On December 6, 2010, EPA published a rule finalizing numeric nutrient criteria for Florida’s 

lakes, springs, and flowing waters outside of the South Florida Nutrient Watershed Region (40 

CFR 131.43). Following publication of the “inland waters rule”, challenges were filed in the U.S. 

District Court for the Northern District of Florida alleging that EPA’s determination and final 
rule were arbitrary, capricious, an abuse of discretion, and not in accordance with the law for a 

variety of reasons.

Along with the inland waters rule, EPA developed an economic analysis to provide the public 

with information on potential costs and benefits that may be associated with Florida’s 

implementation of EPA’s rule. EPA determined that an independent peer review of the 

approaches used in its economic analysis would provide important information on the disparity 

between EPA’s cost estimates and those of some stakeholders, and would be helpful to inform 

and improve its analysis of this proposed rule for Florida’s estuaries, coastal waters and south 

Florida inland flowing waters. Accordingly, EPA requested the National Research Council 

(NRC) of the National Academies to review EPA’s economic analysis for the final inland waters 

rule.

Summary of Key Changes

1. On February 18, 2012, the Court upheld EPA’s January 2009 determination and the final 

numeric nutrient criteria for Florida’s lakes and springs, as well as the SSAC provisions 

and the provisions for calculating downstream protection values (DPVs) using either 

modeling or a default option for an impaired lake that is not attaining its numeric nutrient 

criteria. With regard to EPA’s numeric nutrient criteria for flowing waters (i.e., streams) 

and the default option to calculate DPVs for unimpaired lakes based on ambient stream 

nutrient concentrations at the point of entry to the lake, the Court found that EPA had not 

provided sufficient information in its final rule explaining why or how the criteria or 

DPV protect against harmful increases, as opposed to any increase, in nutrients. Thus, the 

Court invalidated these two aspects of EPA’s final rule and remanded them to the Agency 

for further action.

a. EPA and OMB agreed that EPA should review the Court’s ruling on the final 

inland waters rule and, where relevant, ensure that the criteria proposed in this 

proposed rule protect against harmful increases, as opposed to any increase, in 

nutrients.

2. The NRC Committee completed its “Review of the EPA’s Economic Analysis of Final 

Water Quality Standards for Nutrients for Lakes and Flowing Waters in Florida” in June 

2012. 

a. EPA and OMB agreed that EPA should review the NRC report and address the 

NRC recommendations and suggestions in the analysis of costs for the coastal and 

estuary criteria in this proposed rule.

3. On June 13, 2012, Florida submitted new and revised WQS for review by the EPA 

pursuant to section 303(c) of the CWA. EPA approved the provisions of these rules 

submitted for review that constitute new or revised WQS. Among the newly-approved 

State WQS are numeric criteria for nutrients that apply to a set of estuaries and coastal 

marine waters in Florida. Under the Consent Decree, EPA is relieved of its obligation to 

propose numeric criteria for these waters. 

a. EPA and OMB agreed that these waters should not be included in this proposed 

rule, so they were removed from the version that was originally submitted to 

OMB on February 7, 2012.

Attachment
Page 1 of 221

ENVIRONMENTAL PROTECTION AGENCY

40 CFR Part 131

[EPA-HQ-OW-2010-0222; FRL-XXXX-X]

RIN 2040-AF21 

Water Quality Standards for the State of Florida’s Estuaries, Coastal Waters, and 

South Florida Inland Flowing Waters

AGENCY: Environmental Protection Agency (EPA).

ACTION: Proposed rule.

SUMMARY: The U.S. Environmental Protection Agency (EPA or Agency) is proposing 

numeric water quality criteria to protect ecological systems, and aquatic life, and human 

health from nitrogen and phosphorus pollution in estuaries and coastal waters within the 

State of Florida not covered by EPA-approved State rulemaking, and south Florida inland 

flowing waters. These proposed criteria apply to Florida waters that are designated as 

Class I, Class II, or Class III waters and they are intended to protect these designated uses 

as well as implement for the purposes of the Clean Water Act the State’s narrative 

nutrient provision at Subsection 62-302.530(47)(b), Florida Administrative Code 

(F.A.C.), which provides that “[i]n no case shall nutrient concentrations of a body of 

water be altered so as to cause an imbalance in natural populations of aquatic flora or 

fauna.”

DATES: Comments must be received on or before [INSERT DATE 60 DAYS AFTER 

PUBLICATION IN THE FEDERAL REGISTER]. Because of EPA’s obligation to

sign a notice of final rulemaking on or before September 30, 2013 under Consent Decree, 

the Agency regrets that it will be unable to grant any requests to extend this deadline.

Comment [E1]: OMB edit accepted.
Page 2 of 221

ADDRESSES: Submit your comments, identified by Docket ID No. EPA-HQ-OW2010-0222, by one of the following methods:

1. www.regulations.gov: Follow the on-line instructions for submitting comments.

2. Email: ow-docket@epa.gov

3. Mail to: Water Docket, U.S. Environmental Protection Agency, Mail code: 

2822T, 1200 Pennsylvania Avenue, NW, Washington, DC 20460, Attention: 

Docket ID No. EPA-HQ-OW-2010-0222.

4. Hand Delivery: EPA Docket Center, EPA West Room 3334, 1301 Constitution 

Avenue, NW, Washington, DC 20004, Attention Docket ID No. EPA-HQ-OW2010-0222. Such deliveries are only accepted during the Docket’s normal hours 

of operation, and special arrangements should be made for deliveries of boxed 

information.

Instructions: Direct your comments to Docket ID No. EPA-HQ-OW-2010-0222. EPA’s 

policy is that all comments received will be included in the public docket without change 

and may be made available online at www.regulations.gov, including any personal 

information provided, unless the comment includes information claimed to be 

Confidential Business Information (CBI) or other information whose disclosure is 

restricted by statute. Do not submit information that you consider to be CBI or otherwise 

protected through www.regulations.gov or e-mail. The www.regulations.gov Web site is 

an “anonymous access” system, which means EPA will not know your identity or contact 

information unless you provide it in the body of your comment. If you submit an 

electronic comment, EPA recommends that you include your name and other contact 
Page 3 of 221

information in the body of your comment and with any disk or CD-ROM you submit. If 

EPA cannot read your comment due to technical difficulties and cannot contact you for 

clarification, EPA may not be able to consider your comment. Electronic files should 

avoid the use of special characters, any form of encryption, and be free of any defects or 

viruses. For additional information about EPA’s public docket visit the EPA Docket 

Center homepage at http://www.epa.gov/epahome/dockets.htm. 

Docket: All documents in the docket are listed in the www.regulations.gov index.

Although listed in the index, some information is not publicly available, e.g., CBI or 

other information whose disclosure is restricted by statute. Certain other material, such as 

copyrighted material, will be publicly available only in hard copy. Publicly available 

docket materials are available either electronically in www.regulations.gov or in hard 

copy at a docket facility. The Office of Water (OW) Docket Center is open from 8:30

a.m. until 4:30 p.m., Monday through Friday, excluding legal holidays. The OW Docket 

Center telephone number is (202) 566-2426, and the Docket address is OW Docket, EPA 

West, Room 3334, 1301 Constitution Avenue, NW, Washington, DC 20004. The Public 

Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding 

legal holidays. The telephone number for the Public Reading Room is (202) 566-1744.

FOR FURTHER INFORMATION CONTACT: Erica Fleisig, U.S. EPA 

Headquarters, Office of Water, Mailcode: 4305T, 1200 Pennsylvania Avenue, NW, 

Washington, DC 20460; telephone number: (202) 566-1057; email address: 

fleisig.erica@epa.gov.
Page 4 of 221

SUPPLEMENTARY INFORMATION: This supplementary information section is 

organized as follows: 

Table of Contents

I. General Information

A. Executive Summary

B. Which Water Bodies Are Affected By This Rule?

C. What Entities May Be Affected By This Rule?

D. What Should I Consider as I Prepare My Comments for EPA?

E. How Can I Get Copies of This Document and Other Related Information?

II. Background

A. Nitrogen and Phosphorus Pollution

B. Statutory and Regulatory Background

C. Water Quality Criteria

D. EPA Determination Regarding Florida and Consent Decree

E. EPA’s Rulemaking and Subsequent Litigation

F. Florida Adoption of Numeric Nutrient Criteria and EPA Approval

III. Proposed Numeric Criteria for Florida’s Estuaries, Coastal Waters, and 

South Florida Inland Flowing Waters

A. General Information and Approaches

B. Proposed Numeric Criteria for Estuaries

C. Proposed Numeric Criteria for Coastal Waters

D. Proposed Numeric Criteria for South Florida Inland Flowing Waters

E. Applicability of Criteria When Final
Page 5 of 221

IV. Under What Conditions Will EPA Either Not Finalize or Withdraw These 

Federal Standards?

V. Alternative Regulatory Approaches and Implementation Mechanisms

A. Designating Uses

B. Variances

C. Site-Specific Alternative Criteria

D. Compliance Schedules

VI. Economic Analysis 

A. Incrementally Impaired Waters

B. Point Source Costs

C. Non-point Source Costs

D. Governmental Costs

E. Summary of Costs

F. Benefits

VII. Statutory and Executive Order Reviews

A. Executive Orders 12866 (Regulatory Planning and Review) and 13563 

(Improving Regulation and Regulatory Review)

B. Paperwork Reduction Act

C. Regulatory Flexibility Act

D. Unfunded Mandates Reform Act

E. Executive Order 13132 (Federalism)

F. Executive Order 13175 (Consultation and Coordination with Indian Tribal 

Governments)
Page 6 of 221

G. Executive Order 13045 (Protection of Children From Environmental 

Health and Safety Risks)

H. Executive Order 13211 (Actions That Significantly Affect Energy Supply, 

Distribution, or Use)

I. National Technology Transfer Advancement Act of 1995

J. Executive Order 12898 (Federal Actions To Address Environmental 

Justice in Minority Populations and Low-Income Populations)

I. General Information

A. Executive Summary

1. Purpose of the Regulatory Action

The primary purpose of this rule is to propose numeric water quality criteria to 

protect ecological systems, and aquatic life, and human health within the State of Florida 

from nitrogen and phosphorus pollution. The criteria proposed in this rule apply to certain 

estuaries and coastal waters within the State of Florida and south Florida inland flowing 

waters (e.g., rivers, streams, canals)1

, with the exception of waters within the lands of the 

Miccosukee and Seminole Tribes, the Everglades Agricultural Area (EAA), and the 

Everglades Protection Area (EvPA).

2

 1 EPA has distinguished south Florida inland flowing waters as waters in the South Florida Nutrient 

Watershed Region (SFNWR). The SFNWR was defined previously in EPA’s final rule for lakes and 

flowing waters as the area south of Lake Okeechobee, the Caloosahatchee River watershed (including 

Estero Bay) to the west of Lake Okeechobee, and the St. Lucie watershed to the east of Lake Okeechobee. 2 FL Statute Section 373.4592 (1994) subsection (2) Definitions: (e) "Everglades Agricultural Area" or 

"EAA" means the Everglades Agricultural Area, which are those lands described in FL Statute Section 

373.4592 (1994) subsection (15).

FL Statute Section 373.4592 (1994) subsection (2) Definitions: (h) "Everglades Protection Area" means 

Water Conservation Areas 1 (which includes the Arthur R. Marshall Loxahatchee National Wildlife 

Refuge), 2A, 2B, 3A, and 3B, and the Everglades National Park.

Comment [E2]: OMB edits accepted.
Page 7 of 221

The criteria support implementation of pollution control programs authorized 

under the Clean Water Act (CWA). As part of a comprehensive program to restore and 

protect the Nation’s waters, Section 303(c) of the CWA directs states to adopt water 

quality standards for their navigable waters. CWA Section 303(c)(2)(A) and EPA's 

implementing regulations at 40 CFR 131 require that state water quality standards include 

the designated use (e.g. public water supply, propagation of fish and wildlife, recreational 

purposes) and criteria that protect those uses. Criteria may be numeric or narrative in 

form, but consistent with EPA regulations at 40 CFR 131.11(a)(1), such criteria “must be 

based on sound scientific rationale and must contain sufficient parameters or constituents 

to protect the designated use.” EPA regulations at 40 CFR 131.10(b) also provide that 

“[i]n designating uses of a water body and the appropriate criteria for those uses, the state 

shall take into consideration the water quality standards of downstream waters and ensure 

that its water quality standards provide for the attainment and maintenance of the water 

quality standards of downstream waters.” The CWA requires that any new or revised 

water quality standards developed by states be submitted to EPA for review and approval 

or disapproval, and authorizes the EPA Administrator to determine, even in the absence 

of a state submission, that a new or revised standard is needed to meet CWA 

requirements.

Florida is known for its abundant and aesthetically beautiful natural resources, 

particularly its aquatic resources, which are very important to Florida’s economy. 

Florida’s coastal and estuarine waters play an especially important part in sustaining the 

environment and the economy in the State. For example, Florida’s saltwater sport fishing 

industry contributes over $5 billion to the State’s economy and more than 54,000 jobs 

Comment [E3]: Paragraph added per OMB 

request.

Comment [E4]: OMB edit accepted.
Page 8 of 221

annually; the State's commercial saltwater fishing industry contributes over $1 billion and 

more than 10,000 jobs annually.3 In 2007, nearly 11.3 million residents and 46.3 million 

visitors participated in recreational saltwater beach activities in Florida. Nearly 3.5 

million residents and approximately 1.4 million visitors used saltwater boat ramps, over 

4.2 million residents and about 3 million visitors participated in saltwater non-boat 

fishing, and over 2.6 million residents and almost 1 million visitors participated in 

canoeing and kayaking. 4

However, nitrogen and phosphorus pollution has contributed to serious water 

quality degradation affecting these coastal and estuarine resources in the State of Florida, 

as well as other Florida waters. Many people throughout Florida, whose livelihood 

depends on these recreational water activities, lose income when recreation, tourism, or 

fishing activities are adversely affected by nitrogen and phosphorus pollution. In the most 

recent Florida Department of Environmental Protection (FDEP) water quality assessment 

report, the Integrated Water Quality Assessment for Florida: 2012 305(b) Report and 

303(d) List Update, FDEP describes widespread water quality impairment in Florida due 

to nitrogen and phosphorus pollution. FDEP’s 2012 report identifies approximately 1,918 

miles of rivers and streams (about 14 percent of assessed river and stream miles), 378,435

acres of lakes (about 31 percent of assessed lake acres), 754 square miles (482,560 acres) 

of estuaries (about 14 percent of assessed estuarine area) and 102 square miles (65,280 

 3 FFWCC. 2011. The economic impact of saltwater fishing in Florida. Florida Fish and Wildlife 

Conservation Commission. <http://myfwc.com/conservation/value/saltwater-fishing>. Accessed December 

2011.

4 FDEP. 2008. Chapter 5 – Outdoor Recreation Demand and Need. In Outdoor Recreation in Florida, 

2008: Florida’s Comprehensive Outdoor Recreation Plan, Final Draft. Florida Department of 

Environmental Protection, Division of Recreation and Parks, Tallahassee, FL. 

<http://www.dep.state.fl.us/parks/planning/forms/SCORP5.pdf>. Accessed December 2011.

Comment [E5]: OMB edit accepted (changed 

from ‘aquatic’)

Comment [E6]: OMB edit accepted.

Comment [E7]: OMB edit accepted.

Comment [E8]: OMB edit accepted.
Page 9 of 221

acres) of coastal waters (about 1.6 percent of assessed coastal waters) as impaired by

nutrients. In addition, the same report indicates that 1,108 miles of rivers and streams 

(about 8 percent of assessed river and stream miles) and 107 square miles (68,480 acres) 

of lakes (about 5 percent of assessed lake square miles) are impaired due to nutrient 

pollution.These numbers may underestimate the miles and acres of nutrient impaired 

waters (though not necessarily the total percentages) in Florida as only 58 percent of 

Florida’s rivers and streams, 82 percent of Florida’s lakes, and 93 percent of Florida’s

estuaries were assessed. 5

On January 14, 2009, EPA determined under CWA section 303(c)(4)(B) that new 

or revised water quality standards (WQS) in the form of numeric nutrient water quality 

criteria are necessary to protect the designated uses that Florida has set for its Class I, 

Class II, and Class III waters. Subsequently, EPA entered into a Consent Decree with 

Florida Wildlife Federation, Sierra Club, Conservancy of Southwest Florida, 

Environmental Confederation of Southwest Florida, and St. Johns Riverkeeper, effective 

on December 30, 2009, which established a schedule for EPA to propose and promulgate 

numeric nutrient criteria for Florida’s lakes, flowing waters, estuaries, and coastal waters. 

The Consent Decree also provided that if Florida submitted and EPA approved numeric 

nutrient criteria for any relevant waterbodies before the dates outlined in the schedule, 

EPA would no longer be obligated to propose or promulgate criteria for those 

waterbodies.

 5 FDEP. 2012. Integrated Water Quality Assessment for Florida: 2012 305(b) Report and 303(d) List

Update. (May 2012). Florida Department of Environmental Protection, Division of Environmental 

Assessment and Restoration, Tallahassee, FL. 

<http://www.dep.state.fl.us/water/docs/2012_integrated_report.pdf>. Accessed August 2012.

Comment [E9]: OMB edits accepted.
Page 10 of 221

On June 13, 2012, FDEP submitted new and revised WQS for review by the EPA 

pursuant to section 303(c) of the CWA. These new and revised WQS are set out primarily 

in Rule 62-302 of the F.A.C. [Surface Water Quality Standards]. FDEP also submitted 

amendments to Rule 62-303, F.A.C. [Identification of Impaired Surface Waters], which 

sets out Florida’s methodology for assessing whether waters are attaining State WQS. On 

November 30, 2012, EPA approved the provisions of these rules submitted for review 

that constitute new or revised WQS (hereafter referred to as the “newly-approved State 

WQS”).

Among the newly-approved State WQS are numeric criteria for nutrients that 

apply to a set of estuaries and coastal marine waters in Florida. Specifically, these newlyapproved State WQS apply to Clearwater Harbor/St. Joseph Sound, Tampa Bay, Sarasota

Bay, Charlotte Harbor/Estero Bay, Clam Bay, Tidal Cocohatchee River/Ten Thousand 

Islands, Florida Bay, Florida Keys, and Biscayne Bay.6 Under the Consent Decree, EPA 

is relieved of its obligation to propose numeric criteria for these waters.

Finally, as described in EPA’s November 30, 2012 approval of Florida’s new or 

revised WQS, while EPA believes that the provisions addressing downstream protection 

will provide for quantitative approaches to ensure the attainment and maintenance of 

downstream waters consistent with 40 CFR 131.10(b), the provisions themselves do not 

consist of numeric values. Because EPA is currently subject to a Consent Decree deadline 

to sign a rule proposing numeric downstream protection values (DPVs) for Florida by 

November 30, 2012, EPA is proposing numeric DPVs to comply with the Consent 

 6 Clam Bay, Tidal Cocohatchee River/Ten Thousand Islands, Florida Bay, Florida Keys, and Biscayne Bay 

are collectively referred to in this proposed rule as “south Florida marine waters,” as these are the 

predominantly marine waters downstream of the South Florida Nutrient Watershed Region.
Page 11 of 221

Decree. However, EPA has amended its January 2009 determination to specify that 

numeric criteria for downstream protection are not necessary and that quantitative 

approaches designed to ensure the attainment and maintenance of downstream water 

quality standards, such as those established by Florida, are sufficient to meet CWA 

requirements. As such, EPA will ask the court to modify the Consent Decree consistent 

with the Agency’s amended determination, i.e., to not require EPA to promulgate 

numeric DPVs for Florida. Accordingly, EPA approved the State’s downstream 

protection provisions subject to the district court modifying the Consent Decree to not 

require EPA to promulgate numeric DPVs for Florida. If the district court agrees to so 

modify the Consent Decree, EPA will not promulgate numeric DPVs for Florida. 

However, if the district court declines to so modify the Consent Decree, EPA would 

intend to promulgate numeric DPVs for Florida and would also expect to revisit its 

November 30, 2012 approval of the State Rule’s downstream protection provisions to 

modify or withdraw its approval. Therefore, EPA has also reserved its authority to do so 

in its approval document.

A full description of all of EPA’s recent actions on Florida numeric nutrient 

criteria and related implications for EPA’s own rules can be found at 

http://water.epa.gov/lawsregs/rulesregs/florida_index.cfm. 

EPA is proposing these numeric criteria in accordance with the terms of the 

January 14, 2009 determination, December 2009 Consent Decree, and subsequent 

revisions to that Consent Decree that require the EPA Administrator to sign this proposal 

by November 30, 2012 (discussed in more detail in Section II.D). EPA believes that the 

Comment [E10]: OMB edit accepted.

Comment [E11]: OMB edit accepted.
Page 12 of 221

proposed criteria in this rule will assure protection of Florida’s existing designated uses 

and are based on sound and substantial scientific data and analyses.

2. Summary of the Major Provisions of the Regulatory Action

To develop these proposed numeric nutrient criteria for Florida’s estuaries, 

coastal waters, and south Florida inland flowing waters, the Agency conducted a detailed 

scientific analysis of the substantial amount of water quality data available from Florida’s

extensive monitoring data set. 

EPA concluded that an approach using relevant biological endpoints and multiple 

lines of evidence including stressor-response analyses and mechanistic modeling was a 

strong and scientifically sound approach for deriving numeric nutrient criteria for 

estuaries, in the form of total nitrogen (TN), total phosphorus (TP) and chlorophyll a

concentrations. EPA’s methodology and the resulting proposed estuarine numeric 

nutrient criteria are presented in more detail in Section III.B of this notice of proposed 

rulemaking. 

For coastal waters on the Atlantic and Gulf coasts of Florida, EPA is proposing to 

use a reference condition-based approach. EPA chose to use satellite remote sensing in all 

coastal areas of Florida except the Big Bend Coastal region. Using this approach, EPA 

developed chlorophyll a criteria from satellite remote sensing imagery and field data to 

calibrate the satellite remote sensing imagery. In the Big Bend Coastal region of Florida7

, 

where satellite remote sensing predictions of chlorophyll a were not possible due to 

reflectance that interferes with the remote sensing imagery in that area, EPA used 

mechanistic and statistical models to determine TN, TP, and chlorophyll a criteria for 

 7 This area includes waters offshore of Apalachicola Bay, Alligator Harbor, Ochlockonee Bay, Big 

Bend/Apalachee Bay, Suwannee River, and Springs Coast.
Page 13 of 221

these coastal waters.8 EPA’s methodology and results for its proposed coastal criteria are 

presented in more detail in Sections III.B and III.C.

EPA is proposing numeric nutrient criteria to ensure the attainment and 

maintenance of the water quality standards in downstream estuaries and south Florida 

marine waters pursuant to the provisions of 40 CFR 131.10(b). EPA examined a variety 

of modeling techniques and data to assess whether waters entering an estuary protect the 

water quality standards within the estuary. Accordingly, EPA is proposing an approach to 

derive TN and TP criteria expressed as downstream protection values (DPVs) at the 

points where inland flowing waters flow into estuaries, or marine waters in south Florida 

(referred to as ‘pour points’). These proposed DPVs apply to all flowing waters, 

including south Florida inland flowing waters (with the exception of waters within the 

lands of the Miccosukee and Seminole Tribes, EAA, and EvPA), that flow directly into 

estuaries or south Florida marine waters. EPA’s proposed approach for deriving DPVs at 

the pour points involves an evaluation of water quality in the downstream estuary, water 

quality conditions at the pour point, and selecting a method to derive the DPV values 

based on available data. The proposed approaches for deriving DPVs in flowing waters 

are presented in more detail in Sections III.B and III.D.

Finally, EPA is proposing to extend the approach finalized in 40 CFR 131.43(e)9

to allow development of Site-Specific Alternative Criteria (SSAC) for estuaries, coastal 

 8 EPA derived TN and TP criteria for coastal waters in the Big Bend Coastal region because mechanistic 

models were used in these areas.

9 40 CFR 131.43(e) authorizes the derivation of Federal Site-Specific Alternative Criteria (SSAC) after 

EPA review and approval of applicant submissions of scientifically defensible criteria that meet the 

requirements of CWA section 303(c) and EPA’s implementing regulations at 40 CFR 131.
Page 14 of 221

waters, and south Florida inland flowing waters. EPA’s rationale for extending these 

SSAC provisions is discussed in more detail in Section V.C.

EPA has incorporated sound science, local expertise, and substantial Floridaspecific data throughout the development of these proposed numeric TN, TP, and 

chlorophyll a criteria. EPA relied upon peer-reviewed criteria development 

methodologies,

10 relevant biological endpoints, and a substantial body of scientific 

analysis provided to EPA by FDEP, as well as other federal, State, and local partners 

such as the National Park Service; National Oceanic and Atmospheric Administration 

(NOAA); U.S. Geological Survey (USGS); Tampa Bay, Indian River Lagoon, Sarasota 

Bay and Charlotte Harbor National Estuary Programs; St. Johns River and South Florida 

Water Management Districts; and Florida International University.

EPA sought feedback on the scientific defensibility of the approaches outlined in 

this proposed rule through a Science Advisory Board (SAB) review. 11 The SAB 

assembled a group of eighteen expert panelists to review EPA’s Methods and Approaches 

for Deriving Numeric Criteria for Nitrogen/Phosphorus Pollution in Florida’s Estuaries, 

Coastal Waters, and Southern Inland Flowing Waters.

12 The SAB recommendations13

 10 USEPA. 2000a. Nutrient Criteria Technical Guidance Manual: Lakes and Reservoirs. EPA-822-B-00-

001. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

USEPA. 2000b. Nutrient Criteria Technical Guidance Manual: Rivers and Streams. EPA-822-B-00-002. 

U.S. Environmental Protection Agency, Office of Water, Washington, DC.

USEPA. 2001. Nutrient Criteria Technical Guidance Manual: Estuarine and Coastal Marine Waters.

EPA-822-B-01-003. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

USEPA. 2010. Using Stressor-Response Relationships to Derive Numeric Nutrient Criteria. EPA-820-S10-001. U.S. Environmental Protection Agency, Office of Water, Washington, DC. 11 USEPA-SAB. 2011. Review of EPA’s draft Approaches for Deriving Numeric Nutrient Criteria for

Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. EPA-SAB-11-010. U.S. 

Environmental Protection Agency, Science Advisory Board, Washington, DC.

12 USEPA. 2010. Methods and Approaches for Deriving Numeric Criteria for Nitrogen/Phosphorus 

Pollution in Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. U.S. 

Environmental Protection Agency, Office of Water, Washington, DC.

13 USEPA-SAB. 2011. Review of EPA’s draft Approaches for Deriving Numeric Nutrient Criteria for
Page 15 of 221

strengthened the scientific basis of these proposed numeric nutrient criteria. A number of 

key interest groups presented their comments and views on the underlying science as part 

of the SAB review process. In addition, EPA met with several groups of stakeholders 

with local technical expertise to discuss potential approaches for deriving scientifically 

defensible numeric nutrient criteria. 

3. Costs and Benefits

This is not an economically significant regulatory actionFor the reasons presented 

in this notice, this is not an economically significant regulatory action under Executive 

Order 12866. Under the CWA, EPA’s promulgation of WQS establishes standards that 

the State of Florida implements through the National Pollutant Discharge Elimination 

System (NPDES) permit process for point source dischargers and may also result in new 

or revised requirements for nitrogen and phosphorus pollution treatment controls on other 

sources (e.g., agriculture, urban runoff, and septic systems) through the development of 

Total Maximum Daily Loads (TMDLs) and Basin Management Action Plans (BMAPs).

As a result of this action, the State of Florida will need to ensure that permits it issues and 

Waste Load Allocations (WLAs) issued under TMDLs and BMAPs include any 

limitations on discharges and other sources necessary to comply with the standards 

established in the final rule. In doing so, the State will have considerable discretion and a 

number of choices associated with permit writing (e.g., relating to compliance schedules, 

variances, etc.) and flexibilities built into the TMDL and BMAP process for WLA 

assignment. While Florida’s implementation of the rule may ultimately result in new or 

revised permit conditions for some dischargers and WLA requirements for control on 

 

Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. EPA-SAB-11-010. U.S. 

Environmental Protection Agency, Science Advisory Board, Washington, DC.

Comment [E12]: OMB edit accepted.
Page 16 of 221

other sources, EPA’s action, by itself, does not establish any requirements directly 

applicable to regulated entities or other sources of nitrogen and phosphorus pollution. 

Additionally, Florida already has an existing narrative water quality criterion14 which

requires that nutrients not be present in estuaries and coastal waters in Florida or in south 

Florida inland flowing waters in concentrations that cause an imbalance in natural 

populations of flora and fauna. The proposed criteria in this rule are consistent with and 

serve to implement the State’s existing narrative nutrient provision.

Although the proposed rule does not establish any requirements directly 

applicable to regulated entities or other sources of nutrient pollution, EPA developed an

economic analysis to provide information on potential costs and benefits that may be 

associated with the State implementation requirements that may be necessary to ensure 

attainment of WQS. EPA conducted an analysis to estimate both the increase in the 

number of impaired waters that may be identified as a result of the proposed rule and the 

annual cost of CWA pollution control actions likely to be implemented by the State of 

Florida to assure attainment of applicable State water quality designated uses for these 

waters. It is important to note that the costs and benefits of pollution controls needed to 

attain water quality standards for nutrients for waters already identified as impaired by 

the State (including waters with TMDLs in place and without TMDLs in place) are not 

included in EPA estimates of the cost of the rule. EPA believes that these costs and 

benefits would be incurred in the absence of the current proposed rule and are therefore 

part of the baseline against which the costs and benefits of this rule are measured. EPA’s 

 14 Subsection 62-302.530(47)(b), Florida Administrative Code (F.A.C.), provides that “[i]n no case shall 

nutrient concentrations of a body of water be altered so as to cause an imbalance in natural populations of 

aquatic flora or fauna.”

Comment [A13]: OMB edit accepted.
Page 17 of 221

analysis is fully described in the document entitled Economic Analysis of Proposed Water 

Quality Standards for the State of Florida’s Estuaries, Coastal Waters, and South

Florida Inland Flowing Waters (hereinafter referred to as the Economic Analysis), which 

can be found in the docket and record for this proposed rule. The final conclusion of this 

assessment is that the incremental costs associated with the proposed rule range between 

$239.0 million and $632.4 million per year (2010 dollars) and total monetized benefits 

may be in the range from $39.0 to $53.4 million annually. EPA’s analysis describes 

additional benefits that could not be monetized. EPA has provided estimates of the annual 

costs and benefits; these exceed the $100 million threshold that defines an economically 

significant rule under section 3(f) of Executive Order 12866. However, EPA cautions that 

these estimates cannot be used to determine that this rule is economically significant. The 

direct effect of this rule is to provide Florida with a numeric articulation of its current 

narrative articulation of nutrients criteria, without affecting the resulting level of 

protection offered by the criteria. The estimates of costs and benefits here are indirect 

estimates (costs and benefits associated with controls for waters that would immediately 

be judged to be impaired due to numeric criteria) of the direct effects of this proposed 

rule (decreasing the time to implement TMDLs on impaired waters), and the relationship 

these indirect estimates bear to the true costs and benefits cannot be determined.

B. Which Water Bodies Are Affected By This Rule?

EPA’s proposed rule applies to estuaries and coastal marine waters that have been 

classified by Florida as Class II (Shellfish Propagation or Harvesting) or Class III

(Recreation, Propagation and Maintenance of a Healthy, Well-Balanced Population of 

Fish and Wildlife), including tidal creeks and marine lakes, but excluding the estuarine 

Comment [E14]: OMB edit accepted.

Comment [E15]: OMB edit accepted.
Page 18 of 221

and marine waters contained in Florida’s newly-approved State WQS. This proposed rule 

also applies to south Florida inland flowing waters that have been classified by Florida as 

Class I (Potable Water Supplies) or Class III water bodies pursuant to Section 62-

302.400, F.A.C., excluding wetlands (e.g. sloughs in south Florida) and flowing waters 

within the lands of the Miccosukee and Seminole Tribes, EvPA, or EAA. 15 Pursuant to 

Subsection 62-302.400(4), F.A.C., “Class I, II, and III surface waters share water quality 

criteria established to protect fish consumption, recreation and the propagation and 

maintenance of a healthy, well-balanced population of fish and wildlife.” 16 Florida 

currently has a narrative nutrient criterion at Subsection 62-302.530(47)(b), F.A.C.17

established to protect these three uses and EPA is numerically interpreting Florida’s 

narrative criterion for the purpose of protecting the Class I, II, and III surface waters for 

the purposes of the CWA in this proposed rulemaking.

EPA is not proposing to change any of Florida’s water body classifications with 

this regulation. The proposed criteria in this regulation would only apply to water bodies 

that are currently classified by Florida as Class I, II, or III and not to water bodies with 

other classifications such as Class III limited waters18 for which use attainability analyses 

 15 In this rule, EPA is interpreting the existing State narrative criterion under Subsection 62-302.530(47)(b), 

F.A.C. That criterion applies to Florida waters classified as Class I (Potable Water Supplies), Class II 

(Shellfish Propagation or Harvesting), and Class III Marine and Fresh (Recreation, Propagation and 

Maintenance of a Healthy, Well-Balanced Population of Fish and Wildlife). EPA is not aware of any 

marine waters that Florida has classified as Class I potable water supply. Therefore, for purposes of this 

rule, EPA is interpreting Subsection 62-302.530(47)(b), F.A.C. to protect fish consumption, recreation, and 

the propagation and maintenance of a healthy, well-balanced population of fish and wildlife in Florida’s 

Class II and III estuarine and coastal waters.

16 Class I waters also include an applicable nitrate limit of 10 mg/L and nitrite limit of 1 mg/L for the 

protection of human health in drinking water supplies. The nitrate limit applies at the entry point to the 

distribution system (i.e., after any treatment); see Section 62-550, F.A.C., for additional details. 17 “[i]n no case shall nutrient concentrations of a body of water be altered so as to cause an imbalance in 

natural populations of aquatic flora or fauna” 18 Class III limited waters include waters that support fish consumption; recreation or limited recreation; 

and/or propagation and maintenance of a limited population of fish and wildlife; see Chapter 62-302.400(1) 
Page 19 of 221

(UAAs) and SSACs for nutrients have been established, or Class IV canals in Florida’s 

agricultural areas.

EPA is defining estuary to be consistent with Florida’s definition of estuary in 

Section 62-303.200, F.A.C., where “estuary” shall mean “predominantly marine regions 

of interaction between rivers and nearshore ocean waters, where tidal action and river 

flow mix fresh and salt water.” Such areas include bays, mouths of rivers, and lagoons

that have been classified as Class II (Shellfish Propagation or Harvesting) or Class III 

(Recreation, Propagation and Maintenance of a Healthy, Well-Balanced Population of 

Fish and Wildlife) water bodies pursuant to Section 62-302.400, F.A.C., excluding 

wetlands.

EPA is defining coastal waters based on Florida’s definitions of open coastal 

waters and open ocean waters, taking into account that CWA jurisdiction extends to three 

nautical miles from shore.19 EPA’s definition of “coastal waters” is all marine waters that 

have been classified as Class II (Shellfish Propagation or Harvesting) or Class III 

(Recreation, Propagation and Maintenance of a Healthy, Well-Balanced Population of 

Fish and Wildlife) water bodies pursuant to Section 62-302.400, F.A.C., extending to 

three nautical miles from shore that are not classified as estuaries. EPA’s proposed rule 

defines “marine waters” to mean surface waters in which the chloride concentration at the 

surface is greater than or equal to 1,500 milligrams per liter (mg/L). 

 

F.A.C. for more details.

19 While CWA jurisdiction, and therefore EPA’s proposed criteria, extend only to three nautical miles from 

shore (CWA section 502(8)), Florida State jurisdiction extends beyond three nautical miles. Florida’s 

seaward boundary in Gulf of Mexico waters is 3 marine leagues (9 nautical miles) and in Atlantic waters is 

3 nautical miles (Submerged Lands Act of 1953. <http://www.boem.gov/uploadedFiles/submergedLA.pdf>

; UNITED STATES v. FLORIDA, 363 U.S. 121 (1960)). Florida defines open coastal waters as “all gulf or 

ocean waters that are not classified as estuaries or open ocean waters.” Open ocean waters consist of “all 

surface waters extending seaward from the most seaward natural 90-foot (15-fathom) isobath” (Subsection 

62-303.200, F.A.C.).
Page 20 of 221

EPA is defining tidal creeks as relatively small coastal tributaries with variable 

salinity that lie at the transition zone between terrestrial uplands and the open estuary. For 

another subset of marine waters, marine lakes, EPA is proposing to use the definition of 

“marine waters” and the definition of lakes included previously in Water Quality 

Standards for the State of Florida’s Lakes and Flowing Waters (40 CFR 131.43) to 

define a marine lake as a slow-moving or standing body of marine water that occupies an 

inland basin that is not a stream, spring, or wetland.

EPA previously defined “flowing waters” in Water Quality Standards for the 

State of Florida’s Lakes and Flowing Waters (40 CFR 131.43). A flowing water is 

defined as “a free-flowing, predominantly fresh surface water in a defined channel, and 

includes rivers, creeks, branches, canals, freshwater sloughs, and other similar water 

bodies.” Consistent with EPA’s definition in 40 CFR 131.43, EPA defines “canal” for 

this proposed rule to mean a trench, the bottom of which is normally covered by water 

with the upper edges of its two sides normally above water. Also as defined in 40 CFR 

131.43, “predominantly fresh waters” means surface waters in which the chloride 

concentration at the surface is less than 1,500 mg/L. EPA is not proposing criteria for 

areas currently managed by the State as wetlands (such as sloughs in south Florida), 

which are outside the scope of this rulemaking.

20

 20 FDEP. 2001. Chapter 2: Ecological Description. In: Everglades Phosphorus Criterion Technical Support 

Document. Part III: WCA-3/ENP. Florida Department of Environmental Protection, Everglades Technical 

Support Section. <http://www.dep.state.fl.us/water/wqssp/everglades/docs/pctsd/IIIChapter2.pdf>. 

Accessed January, 10, 2011.

Doherty, S.J., C.R. Lane, and M.T. Brown. 2000. Proposed Classification for Biological Assessment of 

Florida Inland Freshwater Wetlands. Report to the Florida Department of Environmental Protection. 

Contract No. WM68 (Development of a Biological Approach for Assessing Wetland Function and 

Integrity). Center for Wetlands, University of Florida, Gainesville, FL.

Ogden, J.C. 2005. Everglades ridge and slough conceptual ecological model. Wetlands 25(4):810-820.
Page 21 of 221

C. What Entities May Be Affected By This Rule?

Citizens concerned with water quality in Florida may be interested in this 

rulemaking. Entities discharging nitrogen or phosphorus to estuaries, coastal waters, and 

flowing waters in Florida could be indirectly affected by this rulemaking because water 

quality standards are used in determining National Pollutant Discharge Elimination 

System (NPDES) permit limits. Examples of categories and entities that may ultimately 

be affected are listed in the following table:

Category Examples of potentially affected entities

Industry Industries discharging pollutants to estuaries, coastal waters and flowing 

waters in the State of Florida.

Municipalities Publicly-owned treatment works discharging pollutants to estuaries, coastal 

waters and flowing waters in the State of Florida.

Stormwater Management 

Districts 

Entities responsible for managing stormwater runoff in the State of Florida.

This table is not intended to be exhaustive, but rather provides a guide for 

entities that may be indirectly affected by this action. Other types of entities not listed in 

the table, such as non-point source contributors to nitrogen and phosphorus pollution in 

Florida’s waters, may be affected through implementation of Florida’s water quality 

standards program (e.g., through Basin Management Action Plans (BMAPs)). Any 

parties or entities conducting activities within Florida watersheds covered by this 

proposed rule, or who depend upon or contribute to the water quality of the estuaries, 

coastal waters, and flowing waters of Florida, may be affected by this rule. To determine 

whether your facility or activities may be affected by this action, you should examine this 

proposed rule. If you have questions regarding the applicability of this action to a

particular entity, consult the person listed in the preceding FOR FURTHER 

INFORMATION CONTACT section.
Page 22 of 221

D. What Should I Consider as I Prepare My Comments for EPA?

1. Submitting CBI. Do not submit confidential business information (CBI) to EPA 

through http://www.regulations.gov or e-mail. Clearly mark the part or all of the 

information that you claim to be CBI. For CBI information in a disk or CD-ROM that 

you mail to EPA, mark the outside of the disk or CD-ROM as CBI and then identify 

electronically within the disk or CD-ROM the specific information that is claimed as 

CBI. In addition to one complete version of the comment that includes information 

claimed as CBI, a copy of the comment that does not contain the information claimed as 

CBI must be submitted for inclusion in the public docket. Information so marked will not 

be disclosed except in accordance with procedures set forth in 40 CFR part 2.

2. Tips for Preparing Your Comments. When submitting comments, remember to:

• Identify the rulemaking by docket number and other identifying information 

(subject heading, Federal Register date, and page number).

• Follow directions--The agency may ask you to respond to specific questions or 

organize comments by referencing a Code of Federal Regulations (CFR) part or 

section number.

• Explain why you agree or disagree; suggest alternatives and substitute language 

for your requested changes.

• Describe any assumptions and provide any technical information and/or data that 

you used.

• If you estimate potential costs or burdens, explain how you arrived at your 

estimate in sufficient detail to allow for it to be reproduced.

• Provide specific examples to illustrate your concerns, and suggest alternatives.
Page 23 of 221

• Make sure to submit your comments by the comment period deadline identified.

Commenters who submitted public comments or scientific information on the portions of 

EPA’s January 26, 2010 proposed Water Quality Standards for the State of Florida’s 

Lakes and Flowing Waters (75 FR 4173) that are addressed in this proposal should 

reconsider their previous comments in light of the new information presented in this 

proposal and must re-submit their comments during the public comment period for this 

rulemaking to receive EPA response.

E. How Can I Get Copies of This Document and Other Related Information?

1. Docket. EPA has established an official public docket for this action under Docket Id. 

No. EPA-HQ-OW-2010-0222. The official public docket consists of the document 

specifically referenced in this action, any public comments received, and other

information related to this action. Although a part of the official docket, the public docket 

does not include CBI or other information whose disclosure is restricted by statute. The 

official public docket is the collection of materials that is available for public viewing at 

the OW Docket, EPA West, Room 3334, 1301 Constitution Ave., NW, Washington, DC 

20004. This Docket Facility is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, 

excluding legal holidays. The Docket telephone number is 202-566-2426. A reasonable 

fee will be charged for copies.

2. Electronic Access. You may access this Federal Register document electronically 

through the EPA Internet under the “Federal Register” listings at

http://www.epa.gov/fedrgstr/. An electronic version of the public docket is available 
Page 24 of 221

through EPA's electronic public docket and comment system, EPA Dockets. You may 

use EPA Dockets at http://www.regulations.gov to view public comments, access the 

index listing of the contents of the official public docket, and to access those documents 

in the public docket that are available electronically. For additional information about 

EPA's public docket, visit the EPA Docket Center homepage at 

http://www.epa.gov/epahome/dockets.htm. Although not all docket materials may be 

available electronically, you may still access any of the publicly available docket 

materials through the Docket Facility identified in Section I.E(1).

II. Background

A. Nitrogen and Phosphorus Pollution

1. What is Nitrogen and Phosphorus Pollution?

a. Overview of Nitrogen and Phosphorus Pollution

Excess loading of nitrogen and phosphorus to surface water bodies and 

groundwater is one of the leading causes of water quality impairments in the United 

States.21 The problem extends to both fresh and marine waters,22 leading to over 15,000 

nutrient pollution-related impairments in 49 states across the country—a figure that may 

substantially understate the problem as many waters have yet to be assessed.23 Estuaries 

 21 Dubrovsky, N.M., K.R. Burow, G.M. Clark, J.M. Gronberg, P.A. Hamilton, K.J. Hitt, D.K. Mueller, 

M.D. Munn, B.T. Nolan, L.J. Puckett, M.G. Rupert, T.M. Short, N.E. Spahr, L.A. Sprague, and W.G. 

Wilber. 2010. The Quality of our Nation’s waters—Nutrients in the Nation’s Streams and Groundwater, 

1992–2004. Circular 1350. U.S. Geological Survey, National Water Quality Assessment Program, Reston, 

VA. < http://water.usgs.gov/nawqa/nutrients/pubs/circ1350>. Accessed December 2011. 22 Smith, V.H., S.B. Joye, and R.W. Howarth. 2006. Eutrophication of freshwater and coastal marine 

ecosystems. Limnology and Oceanography 51(1, part 2):351-355.

Schindler, D.W. 2006. Recent advances in the understanding and management of eutrophication. 

Limnology and Oceanography 51(1, part2):356–363. 23 Nationally, only 27% of rivers and streams and less than 50% of lakes, reservoirs, and ponds have been 

assessed for impairment (USEPA. 2011. National Summary of State Information. U.S. Environmental 
Page 25 of 221

and coastal waters are especially vulnerable to nitrogen and phosphorus pollution because 

they are the ultimate receiving waters for most major watersheds transporting nitrogen 

and phosphorus loadings from multiple upstream sources.24

The problem of nitrogen and phosphorus pollution is not new. Over forty years 

ago, a 1969 report by the National Academy of Sciences25 noted that “[m]an’s activities, 

which introduce excess nutrients, along with other pollutants, into lakes, streams, and 

estuaries, are causing significant changes in aquatic environments. The excess nutrients 

greatly accelerate the process of eutrophication. The pollution problem is critical because 

of increased population, industrial growth, intensification of agricultural production, 

river-basin development, recreational use of waters, and domestic and industrial 

exploitation of shore properties. Accelerated eutrophication causes changes in plant and 

animal life – changes that often interfere with use of water, detract from natural beauty, 

and reduce property values.” A 2000 report by the National Research Council26

concluded that “...scientists, coastal managers, and public decision-makers have come to 

recognize that coastal ecosystems suffer a number of environmental problems that can, at 

times, be attributed to the introduction of excess nutrients from upstream watersheds. The 

problems are caused by a complex chain of events and vary from site to site, but the 

 Protection Agency, Watershed Assessment, Tracking & Environmental Results. 

<http://iaspub.epa.gov/waters10/attains_nation_cy.control>. Accessed January 2012). 24 Bricker, S., B. Longstaff, W. Dennison, A. Jones, K. Boicourt, C. Wicks, and J. Woerner. 2007. Effects 

of Nutrient Enrichment in the Nation’s Estuaries: A Decade of Change. NOAA Coastal Ocean Program 

Decision Analysis Series No. 26. National Centers for Coastal Ocean Science, Silver Spring, MD. 

<http://ccma.nos.noaa.gov/publications/eutroupdate/> Accessed January 2012.

National Research Council. 2000. Clean Coastal Waters: Understanding and Reducing the Effects of 

Nutrient Pollution. Report prepared by the Ocean Study Board and Water Science and Technology Board, 

Commission on Geosciences, Environment and Resources, National Resource Council, Washington, DC. 25 National Academy of Sciences. 1969. Eutrophication: Causes, Consequences, Correctives. National 

Academy of Sciences, Washington, DC. 26 National Research Council. 2000. Clean Coastal Waters: Understanding and Reducing the Effects of 

Nutrient Pollution. Report prepared by the Ocean Study Board and Water Science and Technology Board, 

Commission on Geosciences, Environment and Resources, National Resource Council, Washington, DC.
Page 26 of 221

fundamental driving force is the accumulation of nitrogen and phosphorus in fresh water 

on its way to the sea.” 

Florida has long struggled with nutrient pollution impacts to its surface and 

ground waters. Florida's flat topography makes Florida particularly susceptible to 

nitrogen and phosphorus pollution because water moves more slowly over the landscape, 

allowing time for nitrogen and phosphorus pollution to accumulate in water bodies and 

cause eutrophication. Florida’s high rainfall levels contribute to increased run-off, and 

higher temperatures and sunlight contribute to eutrophication when excess nutrients are 

available.

27

In FDEP’s 2012 Integrated Water Quality Assessment for Florida: 2012 305(b) 

Report and 303(d) List Update, nutrient pollution is ranked as the fifth major cause of 

estuary impairments by impaired square miles28 and the fifth major cause of impairments 

in coastal waters.29 FDEP documents nutrient pollution impairments in 754 square miles 

(482,560 acres) of estuaries (about 14 percent of the estuarine area assessed by Florida) 

and 102 square miles (65,280 acres) of coastal waters (about 1.6 percent of the assessed 

coastal waters).30

 27 Perry, W.B. 2008. Everglades restoration and water quality challenges in south Florida. Ecotoxicology 

17:569-578. 28 First, second, third, and fourth major causes of estuary impairments by impaired square miles are 

mercury in fish, DO, bacteria in shellfish, and fecal coliform, respectively. 29 FDEP. 2012. Integrated Water Quality Assessment for Florida: 2012 305(b) Report and 303(d) List 

Update. (May 2012). Florida Department of Environmental Protection, Division of Environmental 

Assessment and Restoration, Tallahassee, FL. 

<http://www.dep.state.fl.us/water/docs/2012_integrated_report.pdf>. Accessed August 2012. 30 FDEP. 2012. Integrated Water Quality Assessment for Florida: 2012 305(b) Report and 303(d) List 

Update. (May 2012). Florida Department of Environmental Protection, Division of Environmental 

Assessment and Restoration, Tallahassee, FL. 

<http://www.dep.state.fl.us/water/docs/2012_integrated_report.pdf>. Accessed August 2012.
Page 27 of 221

FDEP noted in its 2008 Integrated Water Quality Assessment for Florida: 2008 

305(b) Report and 303(d) List Update that nitrogen and phosphorus pollution poses 

several challenges in Florida. FDEP stated, “The close connection between surface and 

groundwater, in combination with the pressures of continued population growth, 

accompanying development, and extensive agricultural operations, present Florida with a 

unique set of challenges for managing both water quality and quantity in the future. After 

trending downward for 20 years, beginning in 2000 phosphorus levels again began 

moving upward, likely due to the cumulative impacts of non-point source pollution 

associated with increased population and development. Increasing pollution from urban 

stormwater and agricultural activities is having other significant effects.”31

To better understand the nitrogen and phosphorus pollution problem in Florida, 

EPA looked at trends in the data Florida uses to create its Integrated Water Quality 

Reports,32 and found increasing concentrations of nitrogen and phosphorus compounds in 

Florida waters over the 12 year period from 1996-2008. Florida’s Impaired Waters Rule 

(IWR) data indicate that levels of total nitrogen have increased approximately 20 percent

from a state-wide average of 1.06 mg/L in 1996 to 1.27 mg/L in 2008 and average statewide total phosphorus levels have increased approximately 40 percent from an average of 

0.108 mg/L in 1996 to 0.151 mg/L in 2008.

On a national scale, the primary sources of nitrogen and phosphorus pollution can 

be grouped into five major categories: (1) urban and suburban stormwater runoff—

 31 FDEP. 2008. Integrated Water Quality Assessment for Florida: 2008 305(b) Report and 303(d) List 

Update. Florida Department of Environmental Protection, Division of Environmental Assessment and 

Restoration, Tallahassee, FL. <http://www.dep.state.fl.us/water/docs/2008_Integrated_Report.pdf>. 

Accessed July 2011.

32 IWR Run 40. Updated through February 2010.
Page 28 of 221

sources associated with residential and commercial land use and development; (2) 

municipal and industrial wastewater discharges; (3) row crop agriculture and fertilizer 

use; (4) livestock production and manure management practices; and (5) atmospheric 

deposition resulting from nitrogen oxide emissions from fossil fuel combustion and 

ammonia emissions from row crop agriculture and livestock production. Land use and 

land cover in watersheds across much of the nation has been altered such that now a 

higher fraction of nitrogen and phosphorus applied to the landscape reaches surface and 

groundwater resources. These sources contribute loadings of anthropogenic nitrogen and 

phosphorus to surface and groundwaters, and may cause far-reachingharmful impacts to

aquatic ecosystems and imbalances in the natural populations of aquatic flora and 

fauna.33

In general, the major sources of nitrogen and phosphorus pollution in Florida 

estuarine and coastal waters are the same as those found at the national scale: urban and 

suburban stormwater runoff, wastewater discharges, row crop agriculture, livestock 

production, and atmospheric deposition. As is the case with much of the southern United 

States, Florida’s population continues to grow, with Florida among the top ten fastest 

growing states.34 Florida’s population growth is concentrated in major cities and along 

the coast. As of 2005, Florida’s highest population density was along its eastern coast; 

there has also been significant population expansion along the western coast from Tampa 

to the south. As populations grow, the increased nitrogen and phosphorus pollution 

 33 State-EPA Nutrient Innovations Task Group. 2009. An Urgent Call to Action: Report of the State-EPA 

Nutrient Innovations Task Group.

<http://water.epa.gov/scitech/swguidance/standards/criteria/nutrients/upload/2009_08_27_criteria_nutrient

_nitgreport.pdf> Accessed May 2012. 34 U.S. Census Bureau. 2011. Population Distribution and Change: 2000 to 2010. 

<http://www.census.gov/prod/cen2010/briefs/c2010br-01.pdf>. Accessed July 2011.

Comment [E16]: OMB edit accepted.

Comment [E17]: OMB edit accepted.

Comment [E18]: OMB edit accepted.
Page 29 of 221

resulting from increased urban stormwater runoff, municipal wastewater discharges, air 

deposition, and agricultural livestock activities and row-crop runoff can place increased 

stress on all ecosystems. 

In nearly half of the estuaries examined for this rulemaking, urban or stormwater 

runoff is a major contributor of nitrogen and phosphorus pollution. For example, a report 

issued in 2010 by the Sarasota Bay Estuary Program indicates that in Sarasota Bay,

nutrients are primarily transported to the estuary by stormwater runoff, which is the 

predominant source in all segments of the estuary (42-60 percent of the total nitrogen 

load).

35 Similarly, according to the Tampa Bay Estuary Program, the largest source of 

nitrogen to Tampa Bay is also runoff (63 percent of total nitrogen loadings to Tampa Bay

from 1999–2003).36 Impervious land cover is a large driver of stormwater volume. In 

2005, one study estimated that 7 percent of Florida’s area had total impervious area 

greater than 20 percent, and of that, a quarter of that land had total impervious area

greater than 40 percent. As Florida’s population grows, it is likely that the resulting 

expansion of impervious cover will cause increased harmful impacts on water quality in

coastal areas, wetlands, and other aquatic ecosystems.37

Wastewater is also a significant contributor of nitrogen and phosphorus pollution. 

In Florida, there are 443 domestic (not including septic systems) and industrial 

 35 SBEP. 2010. Numeric Nutrient Criteria for Sarasota Bay. Prepared for the Sarasota Bay Estuary 

Program by Janicki Environmental, Inc. <http://www.sarasotabay.org/documents/SBEP-NNC-FinalReport.pdf>. Accessed August 2011.

36 TBEP. No date. About the Tampa Bay Estuary Program, State of the Bay: Water and Sediment Quality. 

Tampa Bay Estuary Program. < http://www.tbep.org/tbep/stateofthebay/waterquality.html>. Accessed 

January 2012.

37 Exum, L.R., S.L. Bird, J. Harrison, and C.A. Perkins. 2005. Estimating and Projecting Impervious Cover 

in the Southeastern United States. EPA/600/R-05/061. U.S. Environmental Protection Agency, Office of 

Research and Development, Washington, DC.

Comment [E19]: OMB edits accepted.

Comment [E20]: OMB edit accepted.
Page 30 of 221

wastewater dischargers with individual NPDES permits.

38 Of those facilities, 198 are 

classified as domestic (municipal) wastewater facilities, which treat sanitary wastewater 

or sewage from homes, businesses, and institutions. The other 245 facilities are classified 

as industrial wastewater facilities. About one third of Florida’s population uses on-site 

sewage treatment and disposal (septic tanks) to treat wastewater.

39

In Florida, fewer than a quarter of individually permitted domestic and industrial 

facilities are authorized to discharge to surface waters. The remaining permittees are 

authorized to discharge solely to groundwater through land-application, beneficial reuse 

of reclaimed water, or deep well injection. Domestic wastewater treatment facilities 

permitted by FDEP produce over 1.5 billion gallons of treated effluent and reclaimed 

water per day, with a total treatment capacity of over 2.5 billion gallons per day. Eighteen 

percent of domestic wastewater treatment facilities have treatment capacities greater than 

500,000 gallons per day, whereas 73 percent of domestic wastewater treatment facilities 

have capacities less than 100,000 gallons per day.40

Wastewater has been cited as contributing to negative impacts on water quality in 

some areas. On the east coast of Florida, septic systems contribute an estimated 1.5 

 38 Facilities with NPDES permits either discharge to surface waters or ground waters, using methods that 

include land application, beneficial reuse of reclaimed water, and deep well injection. USEPA. 2011. 

Permit Compliance System Database. U.S. Environmental Protection Agency. 

<http://www.epa.gov/enviro/facts/pcs/customized.html>. Accessed June 2011.

There are also 34,508 dischargers covered under generic or general permits, which FDEP regulates based 

on categories of wastewater facilities or activities that involve the same or similar types of operations or 

wastes.

39 FDEP. 2011. General Facts and Statistics about Wastewater in Florida. Florida Department of 

Environmental Protection. <http://www.dep.state.fl.us/water/wastewater/facts.htm>. Accessed January 

2012.

40 FDEP. 2011. Wastewater Program. Florida Department of Environmental Protection. 

<http://www.dep.state.fl.us/water/wastewater/index.htm> Accessed January 2012.
Page 31 of 221

million pounds of nitrogen per year to Florida’s Indian River Lagoon.41 There have been 

some successes in reducing the impact of wastewater on marine waters. In Tampa Bay, 

wastewater treatment plants were one of the major sources of nitrogen prior to the 

institution of tertiary nitrogen removal. This treatment has contributed to an improvement 

in Tampa Bay’s water quality.42

There have been a number of studies examining the sources of nitrogen and 

phosphorus pollution in waters across Florida. One area of study is Biscayne Bay, located 

on the southeast coast of Florida, adjacent to Miami. Nutrient pollution in the Bay comes 

from a number of key sources that vary geographically: stormwater runoff from urban 

areas, discharges from the Black Point Landfill and Sewage Treatment Plant, agricultural 

runoff from canals in the South Dade agricultural basin, and contaminated ground

water.43 In the northern section of the Bay, there are inputs from five canals, a landfill, 

and urban runoff. The southern section of the Bay has a greater contribution from 

agricultural sources.44 In one study, researchers found that canals conveying waters from 

agricultural and urban areas contributed 88 percent and 66 percent of the Bay’s total 

dissolved inorganic nitrogen and total phosphorus loads, respectively.45

 41 USEPA. 2003. EPA Voluntary National Guidelines for Management of Onsite and Clustered 

(Decentralized) Wastewater Treatment Systems. EPA-832-B-03-001. U.S. Environmental Protection 

Agency, Office of Water, Washington, DC. <http://www.epa.gov/owm/septic/pubs/septic_guidelines.pdf>. 

Accessed August 2011.

42 Johansson, J.O.R., and H.S. Greening. 2000. Seagrass Restoration in Tampa Bay: A Resource-based 

Approach to Estuarine Management. Chapter 20 In: Seagrasses: Monitoring, Ecology, Physiology, and 

Management, ed. S.A. Bortone, pp. 279–293. CRC Press, Boca Raton, FL. 43 Caccia, V.G., and J.N. Boyer. 2007. A nutrient loading budget for Biscayne Bay, Florida. Marine 

Pollution Bulletin 54(7):994–1008.

Caccia, V.G., and J.N. Boyer. 2005. Spatial patterning of water quality in Biscayne Bay, Florida as a 

function of land use and water management. Marine Pollution Bulletin 50(11):1416–1429. 44 Caccia, V.G., and J.N. Boyer. 2005. Spatial patterning of water quality in Biscayne Bay, Florida as a 

function of land use and water management. Marine Pollution Bulletin 50(11):1416–1429. 45 Caccia, V.G., and J.N. Boyer. 2007. A nutrient loading budget for Biscayne Bay, Florida. Marine 

Pollution Bulletin 54(7):994–1008.
Page 32 of 221

b. Adverse Impacts of Nitrogen and Phosphorus Pollution on Aquatic Life

Nitrogen and phosphorus pollution in surface and ground waters degrade water 

quality and negatively impact aquatic life through processes associated with 

eutrophication.46 Eutrophication is a predictable, well-understood, and widelydocumented biological process by which anthropogenic nitrogen and phosphorus 

pollution results in increased growth of algae (plankton and periphyton).47

 46 Eutrophication is the process by which a water body becomes enriched with organic material, which is 

formed by primary productivity (i.e., photosynthetic activity) and can be stimulated to harmful levels by the 

anthropogenic introduction of high concentrations of nutrients—particularly nitrogen and phosphorus 

(National Research Council. 2000. Clean Coastal Waters: Understanding and Reducing the Effects of 

Nutrient Pollution. Report prepared by the Ocean Study Board and Water Science and Technology Board, 

Commission on Geosciences, Environment and Resources, National Resource Council, Washington, DC. 

See also Nixon. S.W. 1995. Coastal marine eutrophication: A definition, social causes, and future concerns. 

Ophelia 41:199-219.) 47 Cambridge, M.L., J.R. How, P.S. Lavery, and M.A. Vanderklift. 2007. Retrospective analysis of epiphyte 

assemblages in relation to seagrass loss in a eutrophic coastal embayment. Marine Ecology Progress Series

346:97-107.

Frankovich, T.A., and J.W. Fourqurean. 1997. Seagrass epiphyte loads along a nutrient availability 

gradient, Florida Bay, USA. Marine Ecology Progress Series 159:37-50.

Peterson, B.J., T.A. Frankovich, and J.C. Zieman. 2007. Response of seagrass epiphyte loading to field 

manipulations of fertilization, gastropod grazing and leaf turnover rates. Journal of Experimental Marine 

Biology and Ecology 349(1):61-72.

Howarth, R., D. Anderson, J. Cloern, C. Elfring, C. Hopkinson, B. Lapointe, T. Malone, N. Marcus, K.J. 

McGlathery, A. Sharpley, and D. Walker. 2000. Nutrient pollution of coastal rivers, bays, and seas. Issues 

in Ecology 7:1-15.

Cloern, J.E. 2001. Our evolving conceptual model of the coastal eutrophication problem. Marine Ecology 

Progress Series 210:223-253. 

Elser, J.J., M.E.S. Bracken, E.E. Cleland, D.S. Gruner, W.S. Harpole, H. Hillebrand, J.T. Ngai, E.W. 

Seabloom, J.B. Shurin, and J.E. Smith. 2007. Global analysis of nitrogen and phosphorus limitation of 

primary production in freshwater, marine, and terrestrial ecosystems. Ecology Letters 10:1135-1142.

Smith, V.H. 2006. Responses of estuarine and coastal marine phytoplankton to nitrogen and phosphorus 

enrichment. Limnology and Oceanography 51(1, part 2): 377–384.

Vitousek, P.M., J.D. Aber, R.W. Howarth, G.E. Likens, P.A. Matson, D.W. Schindler, W.H. Schlesinger, 

and D.G. Tilman. 1997. Human alteration of the global nitrogen cycle: Sources and consequences. 

Ecological Applications 7(3):737-750. 

Bricker, S.B., J.G. Ferreira, and T. Simas. 2003. An integrated methodology for assessment of estuarine 

trophic status. Ecological Modelling 169(1):39-60.

Bricker, S.B., B. Longstaff, W. Dennison, A. Jones, K. Boicourt, C. Wicks, and J. Woerner. 2008. Effects 

of nutrient enrichment in the nation's estuaries: A decade of change. Harmful Algae 8(1):21-32.

Boyer, J.N., C.R. Kelble, P.B. Ortner, and D.T. Rudnick. 2009. Phytoplankton bloom status: Chlorophyll a

biomass as an indicator of water quality condition in the southern estuaries of Florida, USA. Ecological 

Indicators 9(6, Supplement 1):S56-S67.

Hutchinson, G.E. 1961. The paradox of plankton. American Naturalist 95:137-145.

Piehler, M.F., L.J. Twomey, N.S. Hall, and H.W. Paerl. 2004. Impacts of inorganic nutrient enrichment on 

phytoplankton community structure and function in Pamlico Sound, NC, USA. Estuarine Coastal and Shelf 
Page 33 of 221

Nitrogen and phosphorus pollution increases algal growth that negatively impacts 

many aspects of ecological communities. As algae growth accelerates in response to 

nutrient pollution, there may be negative changes in algal species composition and 

competition among species, leading to harmful, adverse effects, such as the increased 

growth or dominance of toxic or otherwise harmful algal species.48 These harmful algal 

blooms (HABs) can contain undesirable species of diatoms, cyanobacteria, and 

dinoflagellates, which are known to generate toxins that are a threat to both aquatic life 

and recreational activities.49 Many nuisance taxa of algae are also less palatable to 

aquatic organisms that consume phytoplankton, so prolonged HABs can impact the food 

 

Science 61(2):197-209.

Sanders, J.G., S.J. Cibik, C.F. D'Elia, and W.R. Boynton. 1987. Nutrient enrichment studies in a coastal 

plain estuary: changes in phytoplankton species composition. Canadian Journal of Fisheries & Aquatic 

Sciences 44:83-90.

Parsons, T.R., P.J. Harrison, and R. Waters. 1978. An experimental simulation of changes in diatom and 

flagellate blooms. Journal of Experimental Marine Biology and Ecology 32:285-294.

Paerl, H.W. 1988. Nuisance phytoplankton blooms in coastal, estuarine, and inland waters. Limnology and 

Oceanography 33(4):823-847.

Harding, Jr., L.W. 1994. Long-term trends in the distribution of phytoplankton in Chesapeake Bay: roles of 

light, nutrients, and streamflow. Marine Ecology Progress Series 104:267-291.

Richardson, K. 1997. Harmful or Exceptional Phytoplankton Blooms in the Marine Ecosystem. Advances 

in Marine Biology. 31:301-385.

Hagy, J.D., J.C. Kurtz, and R.M. Greene. 2008. An Approach for Developing Numeric Nutrient Criteria for 

a Gulf Coast Estuary. U.S. Environmental Protection Agency, Office of Research and Development, 

National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC., EPA 600R08/004, 44 pp.

48 Paerl, H.W. 1988. Nuisance phytoplankton blooms in coastal, estuarine, and inland waters. Limnology 

and Oceanography 33(4):823-847.

Anderson, D.M., P.M. Glibert, and J.M. Burkholder. 2002. Harmful algal blooms and eutrophication: 

Nutrient sources, composition, and consequences. Estuaries 25(4):704-726.

Anderson, D.M., J.M. Burkholder, W.P. Cochlan, P.M. Glibert, C.J. Gobler, C.A. Heil, R.M. Kudela, M.L. 

Parsons, J.E.J. Rensel, D.W. Townsend, V.L. Trainer, and G.A. Vargo. 2008. Harmful algal blooms and 

eutrophication: Examining linkages from selected coastal regions of the United States. Harmful Algae

8(1):39-53. 49 Anderson, D.M., P.M. Glibert, and J.M. Burkholder. 2002. Harmful algal blooms and eutrophication: 

Nutrient sources, composition, and consequences. Estuaries 25(4):704-726.

Paerl, H.W. 2002. Connecting atmospheric nitrogen deposition to coastal eutrophication. Environmental 

Science & Technology 36(15):323A-326A.

Anderson, D.M., J.M. Burkholder, W.P. Cochlan, P.M. Glibert, C.J. Gobler, C.A. Heil, R.M. Kudela, M.L. 

Parsons, J.E.J. Rensel, D.W. Townsend, V.L. Trainer, and G.A. Vargo. 2008. Harmful algal blooms and 

eutrophication: Examining linkages from selected coastal regions of the United States. Harmful Algae

8(1):39-53.
Page 34 of 221

supply of the overall aquatic community. More than 100 HAB species have been 

identified in the United States.

50

Marine and fresh waters of the United States are increasingly being negatively 

impacted by HABs. 51 HAB toxins have been linked to illnesses and deaths of marine 

animals, including sea lions, turtles, fish, seabirds, dolphins, and manatees.52 Diatoms in 

HABs, such as Pseudo-nitzschia, produce domoic acid.

53 Domoic acid has been shown to 

accumulate in the tissue of mussels, crabs, and fish, causing their predators to become ill 

or die.54 Domoic acid poisoning has been reported as the cause of death of humpback 

whales in the Gulf of Maine in 2003 and sea lions in California's Monterey Bay during 

May and June of 1998.55 Other toxin-producing algal species that have been linked to 

harmful, adverse aquatic life impacts include Pfisteria piscicida, which produces several 

 50 Abbott, G.M., J.H. Landsberg, A.R. Reich, K.A. Steidinger, S. Ketchen, and C. Blackmore. 2009. 

Resource Guide for Public Health Response to Harmful Algal Blooms in Florida. FWRI Technical Report 

TR-14. Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. 

Petersburg, FL. <http://myfwc.com/research/redtide/task-force/reports-presentations/resource-guide-forpublic-health-response-to-harmful-algal-blooms-in-florida/> Accessed June 2011. 51 Dortch, Q., P. Glibert, E. Jewett, and C. Lopez. 2008. Introduction. Chapter 1 In: HAB RDDTT 2

National Workshop Report, A plan for Reducing HABs and HAB Impacts. eds. Q. Dortch, D.M. Anderson, 

D.L. Ayres, and P.M. Glibert, pp. 5-12. Woods Hole, MA. 52 WHOI. 2008. Marine Mammals. Woods Hole Oceanographic Institution. 

<http://www.whoi.edu/redtide/page.do?pid=14215>. Accessed June 2011.

WHOI. 2008. HAB Impacts on Wildlife. Woods Hole Oceanographic Institution. 

<http://www.whoi.edu/redtide/page.do?pid=9682>. Accessed June 2011.

NOAA. 2011. Overview of Harmful Algal Blooms. National Oceanic and Atmospheric Administration,

Center for Sponsored Coastal Ocean Research. 

<http://www.cop.noaa.gov/stressors/extremeevents/hab/default.aspx>. Accessed June 2011.

53 Thessen, A.E., and D.K. Stoecker. 2008. Distribution, abundance and domoic acid analysis of the toxic 

diatom genus Pseudo-nitzschia from the Chesapeake Bay. Estuaries and Coasts 31:664-672. 54 Bushaw-Newton, K.L., and K.G. Sellner. 1999. Harmful Algal Blooms. In: NOAA's State of the Coast 

Report. National Oceanic and Atmospheric Administration, Silver Spring, MD. 

<http://oceanservice.noaa.gov/websites/retiredsites/sotc_pdf/hab.pdf>. Accessed June 2011. 55 MBARI. 2000, January 5. Molecular Probes Link Sea Lion Deaths to Toxic Algal Bloom. MBARI News 

and Information. Monterey Bay Aquarium Research Institute. 

<http://www.mbari.org/news/news_releases/2000/jan06_scholin.html>. Accessed June 2011.
Page 35 of 221

toxins that impact fish and humans56 and the flagellate Heterosigma akashiwo which 

produces an ichthyotoxin that kills fish.

57

Secondly, excessive algal growth as a result of nitrogen and phosphorus pollution 

reduces water clarity, resulting in reduced light availability for macrophytes and 

seagrasses.58 Seagrasses cover approximately 2.7 million acres throughout the State and 

are a central ecological feature of Florida’s dynamic, highly productive marine 

ecosystems.59 A substantial body of scientific research has linked nitrogen and 

phosphorus pollution, and subsequent reduced light availability, to seagrass decline. 

Excessive nutrient inputs increase phytoplankton biomass and thereby increase water 

column light attenuation, which limits the light available for seagrass photosynthesis. 

This results in reduced growth and increased mortality of seagrasses. In addition, nitrogen 

and phosphorus pollution can lead to excess growth of epiphytic algae on seagrasses that 

 56 Waring G.T., E. Josephson, K. Maze-Foley, and P.E. Rosel, eds. 2010. Humpback Whale (Megaptera 

novaeangliae): Gulf of Maine Stock (December 2009). In: U.S. Atlantic and Gulf of Mexico Marine 

Mammal Stock Assessments – 2010, NOAA Technical Memorandum NMFS-NE-219. National Oceanic 

and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, 

Woods Hole, MA. < http://www.nefsc.noaa.gov/publications/tm/tm219/>. Accessed January 2012. 57 Rensel, J.E.J. 2007. Fish kills from the harmful alga Heterosigma akashiwo in Puget Sound: Recent 

blooms and review. Prepared for National Oceanic and Atmospheric Administration, Center for Sponsored 

Coastal Ocean Research, by Rensel Associates Aquatic Sciences, Arlington, Washington, in cooperation 

with American Gold Seafoods, LLC. <http://www.whoi.edu/fileserver.do?id=39383&pt=2&p=29109>. 

Accessed January 2012.

58 Vitousek, P.M., J.D. Aber, R.W. Howarth, G.E. Likens, P.A. Matson, D.W. Schindler, W.H. Schlesinger, 

and D.G. Tilman. 1997. Human alteration of the global nitrogen cycle: Sources and consequences. 

Ecological Applications 7(3):737-750. 

Bricker, S.B., J.G. Ferreira, and T. Simas. 2003. An integrated methodology for assessment of estuarine 

trophic status. Ecological Modelling 169(1):39-60.

Bricker, S.B., B. Longstaff, W. Dennison, A. Jones, K. Boicourt, C. Wicks, and J. Woerner. 2008. Effects 

of nutrient enrichment in the nation's estuaries: A decade of change. Harmful Algae 8(1):21-32.

Boyer, J.N., C.R. Kelble, P.B. Ortner, and D.T. Rudnick. 2009. Phytoplankton bloom status: Chlorophyll a

biomass as an indicator of water quality condition in the southern estuaries of Florida, USA. Ecological 

Indicators 9(6, Supplement 1):S56-S67.

59 FFWCC. 2003. Conserving Florida's Seagrass Resources: Developing a Coordinated Statewide 

Management Program. Florida Fish and Wildlife Conservation Commission, Florida Marine Research 

Institute, St. Petersburg, FL.
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blocks the light available to seagrasses and affects seagrass growth.60 This reduction of 

seagrass communities, in turn, results in harmful, adverse impacts such as destabilization 

of sediments, which causes the release of more nutrients into the water column.61

The role that nitrogen and phosphorus pollution plays in the decline of seagrass 

has been studied extensively in Florida.62 In a report published by USGS in 2001, six of 

nine Florida estuaries located along the Gulf Coast showed declines in seagrass coverage, 

the predominant causes of which were nitrogen and phosphorus pollution, dredging, 

propeller scarring, hydrologic alterations, increased turbidity, and chronic light 

reduction.63 Florida Fish & Wildlife Conservation Commission has noted several areas of 

significant seagrass decline between 1950 and 2000, including 72 percent loss in St.

Joseph Sound, 43 percent loss in the northern section of Biscayne Bay near Miami, 40 

percent loss in Tampa Bay, 30 percent loss in the Indian River Lagoon, and 29 percent 

loss in Charlotte Harbor. These losses coincided with population growth in these 

 60 Duarte, C.M. 1991. Seagrass depth limits. Aquatic Botany 40(4):363-377. 61 Boyer, J.N., C.R. Kelble, P.B. Ortner, and D.T. Rudnick. 2009. Phytoplankton bloom status: Chlorophyll 

a biomass as an indicator of water quality condition in the southern estuaries of Florida, USA. Ecological 

Indicators 9(6, Supplement 1):S56-S67. 62 Dawes, C.J., R.C. Phillips, and G. Morrison. 2004. Seagrass Communities of the Gulf Coast of Florida: 

Status and Ecology, Final Report. Technical Publication #03-04. Florida Fish and Wildlife Conservation 

Commission, Fish and Wildlife Research Institute, and the Tampa Bay Estuary Program, St. Petersburg, 

FL.

Tomasko, D.A., C.A. Corbett, H.S. Greening, and G.E. Raulerson. 2005. Spatial and temporal variation in 

seagrass coverage in Southwest Florida: assessing the relative effects of anthropogenic nutrient load 

reductions and rainfall in four contiguous estuaries. Marine Pollution Bulletin 50:797–805.

Orth, R.J., T.J.B. Carruthers, W.C. Dennison, C.M. Duarte, J.W. Fourqurean, K.L. Heck Jr., A.R. Hughes, 

G.A. Kendrick, W.J. Kenworthy, S. Olyarnik, F.T. Short, M. Waycott, and S.L. Williams. 2006. A global 

crisis for seagrass ecosystems. Bioscience 56:987-996.

Burkholder, J.M., D.A. Tomasko, and B.W. Touchette. 2007. Seagrasses and eutrophication. Journal of 

Experimental Marine Biology and Ecology 350:46-72.

Collado-Vides, L., V.G. Caccia, J.N. Boyer, and J.W. Fourqurean. 2007. Tropical seagrass-associated 

macroalgae distributions and trends relative to water quality. Estuarine, Coastal and Shelf Science 73:680-

694.

63 USGS. 2001. Seagrass Habitat In the Northern Gulf of Mexico: Degradation, Conservation,

and Restoration of a Valuable Resource. 855-R-04-001. U.S. Geological Survey, Gulf of Mexico Habitat 

Program Team. <http://gulfsci.usgs.gov/gom_ims/pdf/pubs_gom.pdf>. Accessed July 2011.
Page 37 of 221

watersheds, and resulted from human activities such as fertilizer use in residential and 

agricultural areas and construction projects which contribute high levels of suspended 

sediments.64 Several studies have attributed declines in seagrass to excess chlorophyll a

and phytoplankton in the water column which can increase light attenuation. One study 

conducted from 1989-1991 found that excess chlorophyll a caused light attenuation of 16 

to 28 percent across Charlotte Harbor and Tampa Bay. In the same study, the authors 

noted an overall improvement in seagrass recolonization and areal cover in Hillsborough 

Bay and other parts of Tampa Bay starting in the late 1980s coinciding with decreased 

nutrient loading, which resulted in decreased concentrations of chlorophyll a and 

increased water clarity.65 A later study, which conducted sampling monthly between June 

1998 and July 1999, estimated that phytoplankton biomass contributed approximately 29

percent of total water column light attenuation in Lemon Bay, Florida. The authors 

predicted a continuation in the potential decline of seagrasses with increased 

urbanization.66

Lastly, excessive algal growth also leads to low dissolved oxygen (DO)

potentially creating hypoxic and anoxic conditions that cannot support aquatic life and 

thereby can change the balance of natural populations of aquatic fauna expected to 

occur.

67 Hypoxia is typically defined as DO < 2 mg/L, and anoxia as DO < 0.1 mg/L.68

 64 FFWCC. 2002. Florida’s Seagrass Meadows: Benefitting Everyone. Florida Fish and Wildlife 

Conservation Commission, St. Petersburg, FL. 

<http://www.sarasotabay.org/documents/seagrassbrochure.pdf>. Accessed July 2011. 65 McPherson, B.F., and R.L. Miller. 1994. Causes of Light Attenuation in Tampa Bay and Charlotte 

Harbor, Southwestern Florida. Water Resources Bulletin 30(1):43-53. 66 Tomasko, D.A., D.L. Bristol, and J.A. Ott. 2001. Assessment of present and future nitrogen loads, water 

quality, and seagrass (Thalassia testudinum) depth distribution in Lemon Bay, Florida. Estuaries

24(6A):926-938. 67 Vitousek, P.M., J.D. Aber, R.W. Howarth, G.E. Likens, P.A. Matson, D.W. Schindler, W.H. Schlesinger, 

and D.G. Tilman. 1997. Human alteration of the global nitrogen cycle: Sources and consequences. 
Page 38 of 221

The cause and effect relationship between nitrogen and phosphorus pollution and marine 

hypoxia is clear and well documented in the scientific literature.

69 Increased nitrogen and 

phosphorus inputs lead to excessive algal growth and organic matter loading to bottom 

waters. Bacterial decomposition of the organic matter consumes oxygen and depletes the 

water column of DO. 70 In estuaries and coastal waters, low DO is one of the most widely 

reported consequences of nitrogen and phosphorus pollution and one of the best 

predictors of a range of biotic impairments.71 Low DO causes negative impacts to aquatic

life ranging from mortality to chronic impairment of growth and reproduction.72 When 

nitrogen and phosphorus pollution creates adverse conditions that result in large hypoxic 

zones, substantial negative changes in fish, benthic, and plankton communities may 

occur.73 This includes avoidance of these areas by fish, mobile benthic invertebrates 

 

Ecological Applications 7(3):737-750. 68 USEPA. 1999. The Ecological Condition of Estuaries in the Gulf of Mexico. EPA 620-R-98-004. U.S. 

Environmental Protection Agency, Office of Research and Development, National Health and 

Environmental Effects Research Laboratory, Gulf Ecology Division, Gulf Breeze, FL.

69 Conley, D., J. Carstensen, R. Vaquer-Sunyer, and C. Duarte. 2009. Ecosystem thresholds with hypoxia. 

Hydrobiologia 629(1):21-29. 

Conley, D.J., H.W. Paerl, R.W. Howarth, D.F. Boesch, S.P. Seitzinger, K.E. Havens, C. Lancelot, and G.E. 

Likens. 2009. Controlling Eutrophication: Nitrogen and Phosphorus. Science 323(5917):1014-1015. 

Diaz, R.J. 2001. Overview of hypoxia around the world. Journal of Environmental Quality 30(2):275-281. 

Diaz, R.J., and R. Rosenberg. 2008. Spreading dead zones and consequences for marine ecosystems. 

Science 321(5891):926-929. 70 Clement, C., S.B. Bricker and D.E. Pirhalla. 2001. Eutrophic Conditions in Estuarine Waters. In: NOAA's 

State of the Coast Report. National Oceanic and Atmospheric Administration, Silver Spring, MD. 

<http://state-of-coast.noaa.gov/bulletins/html/eut_18/eut.html>. Accessed December 2011. 71 Bricker, S.B., J.G. Ferreira, and T. Simas. 2003. An integrated methodology for assessment of estuarine 

trophic status. Ecological Modelling 169(1):39-60.

Bricker, S.B., C.G. Clement, D.E. Pirhalla, S.P. Orlando, and D.R.G. Farrow. 1999. National Estuarine 

Eutrophication Assessment, Effects of Nutrient Enrichment in the Nation's Estuaries. National Oceanic and 

Atmospheric Administration, National Ocean Service, Special Projects Office and the National Centers for 

Coastal Ocean Science. Silver Spring, MD.

72 USEPA. 2001. Nutrient Criteria Technical Guidance Manual, Estuarine and Coastal Marine Waters. 

EPA-822-B-01-003. U.S. Environmental Protection Agency, Office of Water, Washington, DC. 73 Howell, P., and D. Simpson. 1994. Abundance of marine resources in relation to dissolved oxygen in 

Long Island Sound. Estuaries 17(2):394-402. 

Kidwell, D.M., A.J. Lewitus, S. Brandt, E.B. Jewett, and D.M. Mason. 2009. Ecological impacts of 

hypoxia on living resources. Journal of Experimental Marine Biology and Ecology 381(Supplement 1):S1-

S3. 
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migrating from the hypoxic area, and fish kills in some systems when fish and other 

mobile aquatic organisms have nowhere to migrate away from the areas with low DO.

74

This can result in negative changes to the benthic invertebrate community structure of 

estuaries and coastal areas, with increases of organisms more tolerant of low DO.

75 Even 

intermittent hypoxia can cause shifts in the benthic assemblage to favor resistant or 

tolerant organisms, which are less desirable food sources, creating unbalanced benthic 

communities in the hypoxic zone because fish avoid the area.76 When hypoxia extends 

into shallow waters, it affects spawning and nursery areas for many important fish species 

by reducing the habitat available that protects smaller fish and aquatic organisms, 

especially juveniles, from predation.77 Hypoxia has been implicated in a recent increase

and late-summer dominance of hypoxia-tolerant gelatinous zooplankton (jellyfish and 

ctenophores) in the Chesapeake Bay and other eastern estuaries.78 Reduced fishery 

production in hypoxic zones has been documented in the United States and worldwide.79

 74 Howell, P., and D. Simpson. 1994. Abundance of marine resources in relation to dissolved oxygen in 

Long Island Sound. Estuaries 17(2):394-402.

Kidwell, D.M., A.J. Lewitus, S. Brandt, E.B. Jewett, and D.M. Mason. 2009. Ecological impacts of 

hypoxia on living resources. Journal of Experimental Marine Biology and Ecology 381(Supplement 1):S1-

S3. 75 Baker, S., and R. Mann. 1992. Effects of hypoxia and anoxia on larval settlement, juvenile growth, and 

juvenile survival of the oyster Crassostrea virginica. Biological Bulletin 182(2):265-269. 

Baker, S., and R. Mann. 1994. Feeding ability during settlement and metamorphosis in the oyster 

Crassostrea virginica (Gmelin, 1791) and the effects of hypoxia on post-settlement ingestion rates. Journal 

of Experimental Marine Biology and Ecology 181(2):239-253. 

Baker, S.M., and R. Mann. 1994. Description of metamorphic phases in the oyster Crassostrea virginica

and effects of hypoxia on metamorphosis. Marine Ecology Progress Series 104:91-99. 

Baustian, M., and N. Rabalais. 2009. Seasonal composition of benthic macroinfauna exposed to hypoxia in 

the northern Gulf of Mexico. Estuaries and Coasts 32(5):975-983. 

Breitburg, D. 2002. Effects of hypoxia, and the balance between hypoxia and enrichment, on coastal fishes 

and fisheries. Estuaries 25(4):767-781. 76 Kidwell, D.M., A.J. Lewitus, S. Brandt, E.B. Jewett, and D.M. Mason. 2009. Ecological impacts of 

hypoxia on living resources. Journal of Experimental Marine Biology and Ecology 381(Supplement 1):S1-

S3.

77 Breitburg, D. 2002. Effects of hypoxia, and the balance between hypoxia and enrichment, on coastal 

fishes and fisheries. Estuaries 25(4):767-781. 78 Grove, M., and D.L. Breitburg. 2005. Growth and reproduction of gelatinous zooplankton exposed to low 
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Hypoxia and anoxia in bottom waters result in anoxia in the surface sediments, 

which has geochemical consequences including acidification and release of toxic 

hydrogen sulfide, soluble reactive phosphorus, and ammonia.80 The sediment of hypoxic 

zones then becomes a potential source of nutrients that can increase the degree of 

eutrophication. Systems that have had persistent and chronic hypoxia often fail to recover 

quickly even after pollution loadings have been reduced.81 Reduced oxygen also affects a 

variety of other biogeochemical processes that can negatively impact water quality, such 

as the chemical form of metals in the water column.82 

The harmful, adverse impacts of nitrogen and phosphorus pollution on aquatic life 

have been manifested throughout Florida. The State has been negatively impacted by 

algal blooms for many years. Red algae, Laurencia intricata and Spyridia filamentosa; 

brown algae, Dictyota sp. and Sargassum filipendula; and green algae, Enteromorpha sp., 

 

dissolved oxygen. Marine Ecology Progress Series 301:185–198. 79 Diaz, R.J., and R. Rosenberg. 2008. Spreading dead zones and consequences for marine ecosystems. 

Science 321(5891):926-929. 80 Diaz, R.J., and R. Rosenberg. 2008. Spreading dead zones and consequences for marine ecosystems. 

Science 321(5891):926-929.

Kemp, W.M., W.R. Boynton, J.E. Adolf, D.F. Boesch, W.C. Boicourt, G. Brush, J.C. Cornwell, T.R. 

Fisher, P.M. Glibert, J.D. Hagy, L.W. Harding, E.D. Houde, D.G. Kimmel, W.D. Miller, R.I.E. Newell, 

M.R. Roman, E.M. Smith, and J.C. Stevenson. 2005. Eutrophication of Chesapeake Bay: Historical trends 

and ecological interactions. Marine Ecology Progress Series 303:1-29.

McCarthy, M., K. McNeal, J. Morse, and W. Gardner. 2008. Bottom-water hypoxia effects on sediment–

water interface nitrogen transformations in a seasonally hypoxic, shallow bay (Corpus Christi Bay, TX, 

USA). Estuaries and Coasts 31(3):521-531.

Cai , W., X. Hu, W. Huang, M.C. Murrell, J.C. Lehrter, S.E. Lohrenz, W. Chou, W. Zhai, J.T. Hollibaugh, 

Y. Wang, P. Zhao, X. Guo, K. Gundersen, M. Dai, and G. Gong.. 2011. Acidification of subsurface coastal 

waters enhanced by eutrophication. Nature Geoscience 4:766–770. 81 Conley, D.J., J. Carstensen, G. Ærtebjerg, P.B. Christensen, T. Dalsgaard, J.L.S. Hansen, and A.B. 

Josefson. 2007. Long-term changes and impacts of hypoxia in Danish coastal water. Ecological 

Applications 17(sp5):S165-S184.

Diaz, R.J., and R. Rosenberg. 2008. Spreading dead zones and consequences for marine ecosystems. 

Science 321(5891):926-929. 82 Snoeyink, V.L., and D. Jenkins. 1980. Oxidation-Reduction Reactions. Chapter 7 In: Water Chemistry, 

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Page 41 of 221

Codium isthmocladum, and Halimeda sp. grow in the Florida Bay area.83 At times their

increased growth has threatened the commercially important fish, lobster, and shrimp 

nurseries in the area.84 Southern Palm Beach and northern Broward counties have been 

negatively impacted by algal mats made up of Caulerpa species since the 1990s.

Caulerpa species can become overgrown or displace coral, other macroalgae, or sponges. 

Off Palm Beach County, dive operators and fishermen have reported large amounts of 

Caulerpa brachypus driving fish and lobster away from reefs. Researchers in Florida 

(e.g., Florida Sea Grant, University of Florida IFAS Extension, University of Central 

Florida, Tampa Bay Estuary Program) and nationally (e.g., National Sea Grant, NOAA)

are concerned abouthave noted the spread of C. brachypus in Florida’s coastal waters 

because a related green alga (Caulerpa taxifolia) spread along the Mediterranean and 

California coasts, which is illustrative of the potential for future further spread of C. 

brachypus in Florida coastal waters. California is spending millions to eradicate the C.

taxifoliaalga.

85 Gambierdiscus toxicus (a ciguatoxin producer) is found from Palm Beach 

to the Dry Tortugas and Florida Bay and is suspected to have caused fish kills and disease 

events.

86 Blooms of Lyngbya majuscula were reported in Charlotte Harbor, Cedar Key, 

Sebastian Inlet, Sarasota Bay, Tampa Bay, Terra Ceia Bay, Palma Sola, Manatee River, 

 83 Anderson, D.M., ed. 1995. ECOHAB: The Ecology and Oceanography of Harmful Algal Blooms: A 

National Research Agenda. Woods Hole Oceanographic Institution, Woods Hole, MA. 84 Anderson, D.M., ed. 1995. ECOHAB: The Ecology and Oceanography of Harmful Algal Blooms: A 

National Research Agenda. Woods Hole Oceanographic Institution, Woods Hole, MA. 85 Jacoby, C., B. Lapointe, and L. Creswell. No date. Are native and nonindigenous seaweeds overgrowing 

Florida’s east coast reefs? SGEF–156. Florida Sea Grant College Program. 

<http://nsgl.gso.uri.edu/flsgp/flsgpg01015.pdf>. Accessed January 2012.

Jacoby, C., and L. Walters. 2009. Can We Stop "Killer Algae" from Invading Florida? (March 2009 rev.) 

SGEF-155. Florida Sea Grant College Program. <http://edis.ifas.ufl.edu/pdffiles/sg/sg07200.pdf>. 

Accessed April 2012.

86 FFWCC. No date. Gambierdiscus toxicus. Florida Fish and Wildlife Conservation Commission. 

<http://myfwc.com/media/202186/g_toxicus_1054.pdf>. Accessed January 2012.

Comment [E21]: OMB edits accepted.
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and northwest Bradenton in 1999, 2000, and 2002. Lyngbya majuscula can form sizeable, 

floating mats that emit foul odors.87 In 1991, widespread and persistent blooms of 

cyanobacteria in Florida Bay coincided with massive sponge die-offs, which negatively 

impacted the behavior and abundance of populations of juvenile Caribbean spiny 

lobsters.88 Two Pseudo-nitzschia species found in Florida are P. calliantha, which was 

observed at bloom levels in the northern Indian River Lagoon, and P. 

pseudodelicatissima.

89 Pseudo-nitzschia spp. has been observed in Tampa Bay since the 

1960s. Pseudo-nitzschia spp. cause amnesic shellfish poisoning in humans and mortality 

of marine mammals and seabirds.90

In addition to being negatively indirectly impacted by algal toxins and decline of 

seagrass, aquatic life in Florida is directly impacted by hypoxia. In June 2011, a fish kill 

in Marco Island, Florida was attributed to low dissolved oxygen, resulting from a 

“mixed” bloom of non-toxic algae and diatoms.91 Newspapers in Florida regularly report 

 87 FFWCC. No date. Blue-Green Algal Blooms in Coastal Florida; 1999, 2000, and 2002. Florida Fish and 

Wildlife Conservation Commission. < http://myfwc.com/research/redtide/archive/historical-events/bluegreen-algal-blooms-coastal-fl/>. Accessed January 2012. 88 Butler, M.J., J.H. Hunt, W.F. Herrnking, M.J. Childress, R. Bertelsen, W. Sharp, T. Matthews, J.M.

Field, and H.G. Marshall. 1995. Cascading disturbances in Florida Bay, USA: cyanobacteria blooms, 

sponge mortality, and implications for juvenile spiny lobsters Panulirus argus. Marine Ecology Progress 

Series 129:119-125. 89 Phlips, E.J., S. Badylak, M. Christman, J. Wolny, J. Brame, J. Garland, L. Hall, J. Hart, J. Lansberg, M. 

Lasi, J. Lockwood, R. Paperno, D. Scheidt, A. Staples, K. Steidinger. 2011. Scales of temporal and spatial 

variability in the distribution of harmful algae species in the Indian River Lagoon, Florida, USA. Harmful 

Algae 10:277-290.

Phlips, E.J., S. Badylak, S. Youn, and K. Kelley. 2004. The occurrence of potentially toxic dinoflagellates 

and diatoms in a subtropical lagoon, the Indian River Lagoon, Florida, USA. Harmful Algae 3(1):39-49. 90 Badylak, S., E.J. Phlips, P. Baker, J. Fajans, and R. Boler. 2007. Distributions of phytoplankton in 

Tampa Bay estuary, U.S.A. 2002-2003. Bulletin of Marine Science 80(2):295-317.

Lopez, C.B., Q. Dortch, E.B. Jewett, and D. Garrison. 2008. Scientific Assessment of Marine Harmful Algal 

Blooms. Interagency Working Group on Harmful Algal Blooms, Hypoxia, and Human Health of the Joint 

Subcommittee on Ocean Science and Technology, Washington, DC. 

<http://www.cop.noaa.gov/stressors/extremeevents/hab/habhrca/assess_12-08.pdf>. Accessed April 2012. 91 Fish kill in island canals appears over. 2011, June 2. Marconews.com –Marco Eagle. 

<http://www.marconews.com/news/2011/jun/02/dead-fish-bad-smell-permeate-parts-island/?print=1>. 

Accessed January 2012.
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on impacts associated with nitrogen and phosphorus pollution. Recent examples 

includeIn 2010, there were reports of algal blooms and fish kills in the St. Johns River.

92

Spring releases of water from Lake Okeechobee into the St. Lucie Canal resulted in 

floating mats of toxic cyanobacteria, Microcystis aeruginosa, prompting Martin and St. 

Lucie county health departments to issue public health warnings. 93 A large Microcystis

bloom was documented in the Lower St. Johns River in 2005, covering a 100 mi (160

km) stretch from Jacksonville to Crescent City.94 Toxic cyanobacteria Anabaena 

circinalis and Cylindrospermopsis raciborskii have been implicated in fish kills in the 

Lower St. Johns River basin. 95 In addition, in June 2009, a large algal bloom stretching 

more than 14 mi (23 km) was documented in Tampa Bay. This was linked to surface 

water runoff of nutrients and pollutants (e.g., fertilizers, yard waste, animal feces) that 

were washed into the bay from recent heavy rains.96

Numerous algal blooms, some capable of producing toxins, foul odors, and fish 

kills, occurred in Florida coastal areas, estuaries, and canals in 2011. Green algae, known 

 92 Patterson, S. 2010, July 23. St John’s River Looks Sick, Nelson says. The Florida Times Union. 

<http://jacksonville.com/news/metro/2010-07-23/story/st-johns-looks-sick-nelson-says>. Accessed 

September 2010. 

Patterson, S. 2010, July 21. Foam on St. John’s River Churns Up Environmental Interest. The Florida 

Times Union. <http://jacksonville.com/news/metro/2010-07-21/story/foam-st-johns-churns-environmentalquestions>. Accessed October 2010.

93 Killer, E. 2010, June 10. Blue-green Algae Found Floating Near Palm City as Lake Okeechobee 

Releases Continue. TCPalm. <http://www.tcpalm.com/news/2010/jun/10/blue-green-algae-found-floatingnear-palm-city-o/>. Accessed October 2010. 94 Aubel, M., P. D'Aiuto, A. Chapman, D. Casamatta, A. Reich, S. Ketchen, and C. Williams. 2006. BlueGreen Algae in St. Johns River, FL. Lakeline Summer 2006:40-45. 95 Abbott, G. M., J. H. Landsberg, A. R. Reich, K. A. Steidinger, S. Ketchen, and C. Blackmore. 2009. 

Resource Guide for Public Health Response to Harmful Algal Blooms in Florida. FWRI Technical Report 

TR-14. Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. 

Petersburg, FL. <http://myfwc.com/research/redtide/task- force/reports-presentations/resource-guide-forpublic-health-response-to-harmful-algal-blooms-in-florida/>. Accessed June 2011.

<http://www.lsjr.org/pdf/ResourceGuide_FL_algal_blooms_2009.pdf>. Accessed June 2011.

96 Pittman, C. 2009, June 26. Algae bloom one of largest in Tampa Bay history. St. Petersburg Times. 

<http://www.tampabay.com/news/environment/water/article1013322.ece>. Accessed July 2010.

Comment [E22]: OMB edits accepted.
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as June Grass, were found washing onto local beaches on Okaloosa Island. The algae 

adhere to swimmers, cover beaches and hinder fishing. 97

In the Caloosahatchee River and estuary, high algae and salinity levels caused the 

Olga water treatment plant in Lee County to close in May 2011. Customers complained 

about unusual tastes and odors in their drinking water. The blue-green algae bloom 

significantly affected areas from the W.P. Franklin Lock and Dam, upstream through 

Alva and LaBelle, Florida. The bloom caused fish, bird and shellfish mortalities, and 

triggered the Lee County Health Department to issue warnings and advisories on water 

and fish consumption as well as swimming. Toxic blue-green algae species were 

identified in the bloom, including Anabaena, Oscillatoria and Aphanizomenon sp.98

The Indian River Lagoon also experienced large and prolonged algae blooms.

High levels of green algae Resultor sp. were found from Titusville to Melbourne and 

covering the entire Banana River. The algae were thought to be responsible for killing 

hundreds of fish and inhibiting seagrass growth.99 A large rust-colored bloom of 

 97 Tammen, K. 2011, April 20. It’s not even June and the June Grass is Back. Northwest Florida Daily 

News. <http://www.nwfdailynews.com/news/grass-39438-island-okaloosa.html>. Accessed April 2011. 98 Lee Closes a Water Plant; Blame Algae and Saltwater intrusion in Caloosahatchee. 2011, May 19. CBS 

Wink News Now. <http://www.winknews.com/Local-Florida/2011-05-19/Lee-Closes-a-Water-PlantBlame-Algae-and-Salt-water-intrusion-in-Caloosahatchee>. Accessed December 2011.

Lollar, K. 2011, June 6. Bacterial bloom stains waterway up to LaBelle. News-Press.

<http://www.marconews.com/news/2011/jun/02/dead-fish-bad-smell-permeate-parts-island/>. Accessed 

June 2011.

Crisis in the Caloosahatchee: Algal blooms in local waters. 2011, June 8. Sanibel-Captiva Islander. 

<http://sanibel-captiva-islander.com/page/content.detail/id/511872/Crisis-in-the-Caloosahatchee--Algalblooms-in-local-waters.html?nav=5051>. Accessed June 2011.

Warning added for Lee County waters. 2011, June 16. CBS Wink News Now.

<http://www.winknews.com/Local-Florida/2011-06-16/Warning-added-for-Lee-County-waters>. Accessed 

June 2011.

Cornwell, B. 2011, June 22. Algae Bloom doesn’t deter everyone. Fort Meyers Florida Weekly.

<http://fortmyers.floridaweekly.com/news/2011-06-

22/Top_News/Algae_bloom_doesnt_deter_everyone.html>. Accessed June 2011. 99 Florida Today. 2011, July 18. Green algae killing fish, seagrass in northern Indian River Lagoon. 10 

News WTSP – Tampa Bay.< http://www.wtsp.com/rss/article/201465/19/Green-algae-killing-fishseagrass-in-northern-Indian-River-Lagoon>. Accessed December 2011.
Page 45 of 221

Pyrodinium bahamense formed in Old Tampa Bay in August 2011; the bloom stretched 

from Safety Harbor to the Howard Frankland Bridge and was thought to be caused by a 

combination of heat, rain, and fertilizer runoff. 100

c. Adverse Impacts of Nitrogen and Phosphorus Pollution on Human Health

As noted previously in section II.A.1.b, nitrogen and phosphorus pollution have 

been explicitly linked to changes in natural algal species composition including increased 

growth or dominance of toxic or otherwise harmful algal species.101 Toxins produced by 

HABs have been linked, through recreational exposure, to adverse human health impacts 

through ingestion of contaminated seafood, dermal reactions, and respiratory 

problems. 102 Ingestion of seafood that is contaminated with toxins can cause 

 100 Reyes, R. 2011, August 31. Algae bloom continues to grow in Old Tampa Bay. Tampa Bay Online.

<http://www2.tbo.com/news/breaking-news/2011/aug/31/1/algae-bloom-continues-to-grow-in-old-tampabay-ar-254281/>. Accessed December 2011.

Harwell, D. 2011, August 27. Tampa Bay algae bloom threatens the estuary’s fish. St. Petersburg Times.

<http://www.tampabay.com/news/environment/water/tampa-bay-algae-bloom-threatens-the-estuarysfish/1188284>. Accessed August 2011. 101 Paerl, H.W. 1988. Nuisance phytoplankton blooms in coastal, estuarine, and inland waters. Limnology 

and Oceanography 33(4):823-847.

Anderson, D.M., P.M. Glibert, and J.M. Burkholder. 2002. Harmful algal blooms and eutrophication: 

Nutrient sources, composition, and consequences. Estuaries 25(4):704-726.

Anderson, D.M., J.M. Burkholder, W.P. Cochlan, P.M. Glibert, C.J. Gobler, C.A. Heil, R.M. Kudela, M.L. 

Parsons, J.E.J. Rensel, D.W. Townsend, V.L. Trainer, and G.A. Vargo. 2008. Harmful algal blooms and 

eutrophication: Examining linkages from selected coastal regions of the United States. Harmful Algae

8(1):39-53. 102 WHOI. 2006. Harmful Algae and Red Tides Primer. Woods Hole Oceanographic Institution, Woods 

Hole, MA.

Anderson, D.M. 2004. The Growing Problem of Harmful Algae: Tiny plants pose a potent threat to those 

who live in and eat from the sea. Woods Hole Oceanographic Institution. Oceanus Magazine 43(1):1-5.

Graham, J. 2007. Harmful Algal Blooms. Fact Sheet 2006-3147. U.S. Geological Survey, Lawrence, KS

CDC. 2004. About Harmful Algal Blooms. Centers for Disease Control and Prevention, Atlanta, GA

Bronstein, A.C., D.A. Spyker, L.R. Cantilena, Jr., J.L. Green, B.H. Rumack, S.L. Giffin. 2009. 2008 

Annual Report of the American Association of Poison Control Centers’ National Poison Data System 

(NPDS): 26th Annual Report. Clinical Toxicology 48:979–1178.

Landsberg, J., F.Van Dolah, and G. Doucette. 2005. Marine and estuarine harmful algal blooms: Impacts 

on human and animal health. Chapter 8 In: Oceans and Health: Pathogens in the Marine Environment. eds.

S. Belkin and R.R. Colwell, pp.165-215. Springer, New York.

NOAA. 2009. Marine Biotoxins. National Oceanic and Atmospheric Administration, Northwest Fisheries 
Page 46 of 221

gastrointestinal, neurological, cardiovascular, and hepatological illnesses. In some severe 

cases, ingestion of even a small amount of contaminated seafood can result in coma or

death.103 Each year in the United States, incidents of poisoning from marine toxins are 

reported to the CDC.104

Nitrogen and phosphorus pollution has been linked to human health impacts in 

Florida, primarily through illnesses associated with HABs. Although marine HABs occur 

naturally, increased nutrient loadings and pollution have been linked to increased 

occurrence of some types of HABs.105 Significant HAB-caused toxins that have been 

found in Florida’s marine waters include saxitoxins, brevetoxins, ciguatoxins, 

cyanotoxins, domoic acid, and okadaic acid.106

Ciguatoxins lead to Ciguatera fish poisoning (CFP), one of the most commonly 

reported food borne illnesses caused by a marine biotoxin in the United States,107 with 

176 cases reported to U.S. poison centers in 2009 (22 percent of the total reported cases 

of food poisoning from seafood toxins).

108 Ciguatoxins are bioaccumulative, causing 

 

Science Center. <http://www.nwfsc.noaa.gov/hab/habs_toxins/marine_biotoxins/index.html>. Accessed 

December 2011.

Anderson, D., P. Glibert, and J. Burkholder. 2002. Harmful Algal Blooms and Eutrophication: Nutrient 

Sources, Composition, and Consequences. Estuaries 25(4b):704-726. 103 Bushaw-Newton, K.L., and K.G. Sellner. 1999. Harmful Algal Blooms. In: NOAA's State of the Coast 

Report. National Oceanic and Atmospheric Administration, Silver Spring, MD. 

<http://oceanservice.noaa.gov/websites/retiredsites/sotc_pdf/hab.pdf>. Accessed June 2011. 104 CDC. 2005. Marine Toxins: Frequently Asked Questions. Centers for Disease Control and Prevention, 

Atlanta, GA. < http://www.cdc.gov/ncidod/dbmd/diseaseinfo/marinetoxins_g.htm>. Accessed June 2011. 105 Lopez, C.B., Q. Dortch, E.B. Jewett, and D. Garrison. 2008. Scientific Assessment of Marine Harmful 

Algal Blooms. Interagency Working Group on Harmful Algal Blooms, Hypoxia, and Human Health of the 

Joint Subcommittee on Ocean Science and Technology, Washington, DC. 106 Abbott, G.M., J.H. Landsberg, A.R. Reich, K.A. Steidinger, S. Ketchen, and C. Blackmore. 2009. 

Resource Guide for Public Health Response to Harmful Algal Blooms in Florida. FWRI Technical Report 

TR-14. Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. 

Petersburg, FL. <http://myfwc.com/research/redtide/task- force/reports-presentations/resource-guide-forpublic-health-response-to-harmful-algal-blooms-in-florida/>. Accessed June 2011. 107 Dickey, R.W., and S.M. Plakas. 2010. Ciguatera: A public health perspective. Toxicon 56:123-136. 108 Bronstein, A.C., D.A. Spyker, L.R. Cantilena, Jr., J.L. Green, B.H. Rumack, and S.L. Giffin. 2009. 2008 

Annual Report of the American Association of Poison Control Centers’ National Poison Data System 

Comment [E23]: OMB edit accepted.
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gastrointestinal, neurological, or cardiovascular symptoms that vary in intensity. 109 In 

Florida, CFP poses a significant risk to public health.110 One estimate indicates that 

approximately 1,300 cases of CFP (reported and unreported cases) occur annually in 

Florida.111 The Florida Department of Health (FDOH) reported 8 cases of CFP in 2005, 

44 cases in 2006, 34 cases in 2007, and 51 cases in 2008.112

Saxitoxins lead to paralytic shellfish poisoning (PSP), which occurs when humans 

eat shellfish contaminated with saxitoxins. These toxins affect the nervous system and in 

severe cases cause respiratory paralysis.113 Between January 2002 and May 2004, 28 

cases of saxitoxin poisoning associated with puffer fish caught in Florida’s Indian River 

Lagoon (IRL) were reported. In 2002, the Florida Fish and Wildlife Conservation 

Commission banned the commercial and recreational harvest of puffer fish in several 

water bodies in Florida and made that ban permanent in 2004.114 Domoic acid, also 

 

(NPDS): 26th Annual Report. Clinical Toxicology 48:979–1178. 109 McKee D.B., L.E. Fleming, R. Tamer, R. Weisman, and D. Blythe. 2001. Physician diagnosis and 

reporting of ciguatera fish poisoning in an endemic area. In: Harmful Algal Blooms 2000: Proceedings of 

the Ninth International Conference on Harmful Algal Blooms, Hobart, Australia, 7-11 February 2000,,eds. 

G.M. Hallegraeff, S.I. Blackburn, C.J. Bolch, and R.J. Lewis, pp. 451-453. Intergovernmental 

Oceanographic Commission of UNESCO, Paris, France. 110 Abbott,G. M., J. H. Landsberg, A.R. Reich, K.A. Steidinger, S. Ketchen, and C. Blackmore. 2009. 

Resource Guide for Public Health Response to Harmful Algal Blooms in Florida. FWRI Technical Report 

TR-14. Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. 

Petersburg, FL. <http://myfwc.com/research/redtide/task- force/reports-presentations/resource-guide-forpublic-health-response-to-harmful-algal-blooms-in-florida/>. Accessed June 2011. 111 Abbott,G. M., J. H. Landsberg, A.R. Reich, K.A. Steidinger, S. Ketchen, and C. Blackmore. 2009. 

Resource Guide for Public Health Response to Harmful Algal Blooms in Florida. FWRI Technical Report 

TR-14. Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. 

Petersburg, FL. <http://myfwc.com/research/redtide/task- force/reports-presentations/resource-guide-forpublic-health-response-to-harmful-algal-blooms-in-florida/>. Accessed June 2011. 112 Abbott,G. M., J.H. Landsberg, A.R. Reich, K.A. Steidinger, S. Ketchen, and C. Blackmore. 2009. 

Resource Guide for Public Health Response to Harmful Algal Blooms in Florida. FWRI Technical Report 

TR-14. Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. 

Petersburg, FL. <http://myfwc.com/research/redtide/task- force/reports-presentations/resource-guide-forpublic-health-response-to-harmful-algal-blooms-in-florida/>. Accessed June 2011. 113 Landsberg, J., F. Van Dolah, and G. Doucette. 2005. Marine and estuarine harmful algal blooms: 

Impacts on human and animal health. Chapter 8 In: Oceans and Health: Pathogens in the Marine 

Environment. eds. S. Belkin and R.R. Colwell, pp. 165-215. Springer, New York. 114 Abbott, G.M., J.H. Landsberg, A.R. Reich, K.A. Steidinger, S. Ketchen, and C. Blackmore. 2009. 
Page 48 of 221

produced by HABs, can also cause food poisoning, producing symptoms ranging from 

mild gastrointestinal discomfort to permanent brain damage and, in rare cases, death.115

Recreational exposure to toxins from HABs can occur when humans inhale sea 

spray vapor containing fragments of marine algae cells and their associated toxins during

water-related activities such as jet-skiing or boating, causing hay fever-like respiratory 

problems.

116

In addition, elevated levels of nitrate, a byproduct of nitrogen pollution in surface 

waters, can cause public health concerns if the water is a drinking water source, where 117

nitrate is converted to harmful nitrite after ingestion.118 The primary human health 

concern with nitrates and nitrites in drinking water is methemoglobinemia, although 

adverse thyroid effects have been associated with elevated nitrates as well.

119

Methemoglobinemia, or “blue baby syndrome,” as the name implies, most often affects 

infants less than six months old (although adults can also be affected) when the ingested

 

Resource Guide for Public Health Response to Harmful Algal Blooms in Florida. FWRI Technical Report 

TR-14. Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. 

Petersburg, FL. <http://myfwc.com/research/redtide/task- force/reports-presentations/resource-guide-forpublic-health-response-to-harmful-algal-blooms-in-florida/>. Accessed June 2011.

Landsberg, J.H., S. Hall, J.N. Johannessen, K.D. White, S.M. Conrad, J.P. Abbott, L.J. Flewelling, R.W. 

Richardson, R.W. Dickey, E.L.E. Jester, S. M. Etheridge, J.R. Deeds, F.M. Van Dolah, T.A. Leighfield, Y. 

Zou, C.G. Beaudry, R.A. Benner, P.L. Rogers, P.S. Scott, K. Kawabata, J.L. Wolny, and K.A. Steidinger. 

2006. Saxitoxin Puffer Fish Poisoning in the United States, with the First Report of Pyrodinium bahamense

as the Putative Toxin Source. Environmental Health Perspectives 114(10):1502-1507. 115 NOAA. 2009. Marine Biotoxins. National Oceanic and Atmospheric Administration, Northwest 

Fisheries Science Center. <http://www.nwfsc.noaa.gov/hab/habs_toxins/marine_biotoxins/index.html>. 

Accessed December 2011.

116 CDC. 2010. Facts about Cyanobacteria and Cyanobacterial Harmful Algal Blooms. Centers for Disease 

Control and Prevention. <http://www.cdc.gov/hab/cyanobacteria/facts.htm>. Accessed August 2010. 117 FDEP. 1998. Ground-water Quality and Agricultural Land Use in the Polk County Very Intense Study 

Area (VISA). AMR 1998-2. Florida Department of Environmental Protection, Division of Water Facilities. 

<http://www.dep.state.fl.us/water/ monitoring/docs/facts/fs9802.pdf>. Accessed September 2010. 118 Gulis. G., M. Czompolyova, and J.R. Cerhan. 2002. An Ecologic Study of Nitrate in Municipal 

Drinking Water and Cancer Incidence in Trnava District, Slovakia. Environmental Research 88:182–187. 119.Fan, A.M., and V.E. Steinberg. 1996. Health implications of nitrate and nitrite in drinking water: an 

update on methemoglobinemia occurrence and reproductive and development toxicity. Regulatory 

Toxicology and Pharmacology 23(1 Pt 1):35–43.

Comment [E24]: OMB edit accepted.
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nitrate is converted to nitrite in the body that prevents hemoglobin in the blood from 

delivering oxygen effectively throughout the body. Methemoglobinemia is an acute 

disease and symptoms can develop rapidly in infants, usually over a period of days.

Symptoms include shortness of breath and blueness of the skin, and even death in severe 

cases. 120

EPA developed a Maximum Contaminant Level (MCL) of 10 mg/L for nitrate in 

drinking water and an MCL of 1 mg/L for nitrite.121 In the 2010 USGS National WaterQuality Assessment Program report, nitrate concentrations in streams across the U.S. 

exceeded 10 mg/L in 28 percent of streams in agricultural areas and 83 percent of studies 

of shallow ground water. However, the report also found that nitrate concentrations 

exceeding the MCL of 10 mg/L were more prevalent in groundwater drinking water 

sources than in streams.122 Nitrates are found in groundwater and wells in Florida, 

ranging from the detection limit of 0.02 mg/L to over 20 mg/L. Elevated nitrate 

concentrations in groundwater are more common in rural agricultural areas which are 

often served by private wells. When nitrate occurs at concentrations greater than 1 mg/L, 

it is considered to be the result of human activities such as application of agricultural 

 120 Manassaram, D.M., L.C. Backer, and D.M. Moll. 2006. A Review of Nitrates in Drinking Water:

Maternal Exposure and Adverse Reproductive and Developmental Outcomes. Environmental Health

Perspectives 114(3):320–327.

FDEP. 2011. Drinking Water: Inorganic Contaminants. Florida Department of Environmental Protection. 

<http://www.dep.state.fl.us/water/drinkingwater/inorg_con.htm>. Accessed November 2011. 121 USEPA. 2007. Nitrates and Nitrites: TEACH Chemical Summary. U.S. Environmental Protection

Agency. <http://www.epa.gov/teach/chem_summ/Nitrates_summary.pdf>. Accessed May 2012. 122 Dubrovsky, N.M., K.R. Burow, K.R., G.M. Clark, G.M., J.M. Gronberg, J.M., P.A. Hamilton P.A., K.J.

Hitt, K.J., D.K. Mueller, D.K., M.D. Munn, M.D., B.T. Nolan, B.T., L.J. Puckett, L.J., M.G. Rupert, M.G.,

T.M. Short, T.M., N.E. Spahr, N.E., L.A. Sprague, L.A., and W.G. Wilber, W.G. 2010. The Qquality of our 

Nation’s wWaters—Nutrients in the Nation’s sStreams and gGroundwater, 1992–2004:. Circular 1350. 

U.S. Geological Survey, National Water Quality Assessment Program, Reston, VA. < Circular 1350, 174p. 

http://water.usgs.gov/nawqa/nutrients/pubs/circ1350>. Accessed May 2012.November 2011May 2012.

Comment [E25]: OMB edit accepted.
Page 50 of 221

fertilizers, disposal of animal wastes, and use of septic tanks.123 Monitoring of Florida 

Public Water Supplies from 2004-2011 indicates that exceedances of the nitrate MCL 

reported by drinking water plants in Florida ranged from 19-34 annually.124 A study in 

the late 1980s conducted by Florida Department of Agriculture and Consumer Services 

(FDACS) and FDEP, analyzed 3,949 shallow drinking water wells for nitrate.125 Nitrate 

was detected in 2,483 wells (63%), with 584 wells (15%) above the MCL of 10 mg/L. 

d. Adverse Impacts of Nitrogen and Phosphorus Pollution on the Economy

Excessive algal blooms result in a range of economic losses, including lost 

revenue from impacts to commercial fisheries, recreational fishing and boating trips, and 

tourism, as well as increased drinking water costs and reduced waterfront property 

values. 126 More information concerning the costs and benefits of the numeric nutrient 

criteria proposed in this rule can be found in Section VI.

 123 DeSimone, L.A., P.A. Hamilton, and R.J. Gilliom. 2009. Quality of Water from Domestic Wells in 

Principal Aquifers of the United States, 1991-2004: Overview of Major Findings. Circular 1332.U.S. 

Geological Survey, National Water Quality Assessment Program, Reston, VA. 

<http://water.usgs.gov/nawqa/studies/domestic_wells/WaterWellJournalArticle_DeSimoneetal2009.pdf>. 

Accessed November 2011.

Spechler, R.M. 2010. Hydrogeology and Groundwater Quality of Highlands County, Florida. Scientific 

Investigations Report 2010–5097. U.S. Geological Survey, Reston, VA

Dubrovsky, N.M., K.R. Burow, G.M. Clark, J.M. Gronberg, P.A. Hamilton, K.J. Hitt, D.K. Mueller, M.D. 

Munn, B.T. Nolan, L.J. Puckett, M.G. Rupert, T.M. Short, N.E. Spahr, L.A. Sprague, and W.G. Wilber. 

2010. The Quality of our Nation’s Waters—Nutrients in the Nation’s Streams and Groundwater, 1992–

2004. Circular 1350. U.S. Geological Survey, National Water Quality Assessment Program, Reston, VA. 

<http://water.usgs.gov/nawqa/nutrients/pubs/circ1350>. Accessed May 2012. 124 FDEP. 2012. Chemical Data for 2004, 2005, 2006, 2007, 2008, 2009, 2010, and 2011. Florida 

Department of Environmental Protection. <http://www.dep.state.fl.us/water/drinkingwater/chemdata.htm>. 

Accessed May 2012.

125 Southern Regional Water Program. 2010. Drinking Water and Human Health in Florida. 

<http://srwqis.tamu.edu/florida/program-information/florida-target-themes/drinking-water-and-humanhealth.aspx>. Accessed May 2012.

Obreza, T.A., and K.T. Morgan. 2008. Nutrition of Florida Citrus Trees. 2nd ed. SL 253. University of 

Florida, IFAS Extension. <http://edis.ifas.ufl.edu/pdffiles/SS/SS47800.pdf>. Accessed May 2012. 126 Dodds, W.K., W.W. Bouska, J.L. Eitzmann, T.J. Pilger, K.L. Pitts, A.J. Riley, J.T. Schloesser, and D.J. 

Thornbrugh. 2009. Eutrophication of U.S. Freshwaters: Analysis of Potential Economic Damages.

Comment [E26]: OMB edit accepted.
Page 51 of 221

In 2006, U.S. sportfishers spent $42.0 billion on fishing, including $26.3 billion 

for freshwater fishing and $8.9 billion for saltwater fishing. These costs include triprelated costs (food, lodging), fishing equipment costs, and other costs such as licenses, 

land-leasing, and ownership.127 Commercial harvests of fish and shellfish totaled $3.9 

billion nationally in 2009.128

The economic value of Florida’s marine recreational fisheries is higher than any 

other state in the country. Recreational fishing contributed over $5 billion to Florida’s 

economy in 2006. In the 2008-2009 fiscal year, over 1 million individuals bought a 

marine recreational fishing license, generating over $29 million in revenue.129 Similarly, 

Florida has one of the nation’s top producing commercial fisheries. In 2009, Florida’s

harvest of the top five commercial species of fish and shellfish was worth more than $55 

million combined. In total, commercial fishing contributed more than $1 billion to the 

economy of Florida. Outdoor recreation in Florida (including wildlife-viewing, fishing, 

and water sports) generates $10.1 billion annually.130 In 2006, over 3 million Florida 

residents and 746,000 visitors participated in wildlife-viewing activities, for total retail 

sales of an estimated $3.1 billion.131

 Environmental Science and Technology 43(1):12-19.

129 FFWCC. No Date. The Economic Impact of Saltwater Fishing in Florida. Florida Fish and Wildlife 

Conservation Commission. <http://myfwc.com/conservation/value/saltwater-fishing>. Accessed December 

2011.

130 FFWCC. No Date. Economic Impact of Outdoor Recreation. Florida Fish and Wildlife Conservation 

Commission.

<http://myfwc.com/conservation/value/outdoor-recreation>. Accessed July 2011. 131 USFWS. 2008. 2006 National Survey of Fishing, Hunting, and Wildlife-Associated Recreation: Florida.

FHW/06-FL. U.S. Fish and Wildlife Service. <http://www.census.gov/prod/2008pubs/fhw06-fl.pdf>. 

Accessed July 2011.

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At the county level, Monroe County’s commercial tourism and fishing industries

rely on finfish and shellfish from Florida Bay. Measurable economic losses associated 

with the changing environmental conditions of the Bay have occurred, primarily from the 

substantial decline in pink shrimp harvests due to loss of submerged aquatic vegetation 

(habitat), which was linked to nitrogen and phosphorus pollution as a contributing factor. 

From 1986 through the early 1990s, employment in commercial fishing declined by 

about 10 percent, while income of individuals in the industry declined by $16 million. 

These losses coincided with massive seagrass die-offs in the Bay and blue-green algae 

blooms.

132

HAB toxins can make seafood unsafe for human consumption, leading to an 

overall reduction in the amount of fish purchased due to the real or perceived threats of 

contamination.

133 Additional costs for medical care to treat individuals exposed to toxins 

are also an economic burden associated with HABs. Potential economic impacts from 

nitrogen and phosphorus pollution in Florida include monetary losses due to depressed 

fisheries, tourism and property values, and elevated costs to address nutrient impacts 

(e.g., beach cleanup costs, HAB monitoring). 

Seagrass habitats are valuable components of Florida's estuarine and coastal 

waters. FDEP has estimated that each acre of seagrass is worth $20,255 per year, which 

would translate to a benefit of $44.6 billion statewide.

134 The nearly 2.2 million acres of 

 132 Gorte, R.W. 1994. The Florida Bay economy and changing environmental conditions. 94-435 ENR, 

CRS Report for Congress, Congressional Research Service, The Library of Congress. 133 Anderson, D.M.. 2008. Hearing on “Harmful Algal Blooms: The Challenges on the Nation’s 

Coastlines”. Woods Hole Oceanographic Institution. 

<http://www.whoi.edu/page.do?pid=8916&tid=282&cid=46007>. Accessed December 2011. 134 USGS. 2001. Seagrass Habitat In the Northern Gulf of Mexico: Degradation, Conservation,

and Restoration of a Valuable Resource. U.S. Geological Survey, Gulf of Mexico Habitat Program Team,

855-R-04-001. <http://gulfsci.usgs.gov/gom_ims/pdf/pubs_gom.pdf>. Accessed July 2011.

Comment [E28]: OMB edits accepted.
Page 53 of 221

seagrass beds in Florida’s nearshore waters support fish and shellfish that are 

economically vital to commercial and recreational businesses in Florida.135 Some estuary 

experts have attempted to quantify the overall value of individual estuaries in Florida. For 

example, the Indian River Lagoon National Estuary Program estimated the total value of 

the Indian River Lagoon at $3.7 billion (2009 dollars). In the study, recreational and nonuse values of the lagoon were estimated to increase by nearly $80 million per year (2009 

dollars) if there were a significant increase in the amount and diversity of wildlife in the 

lagoon, as well as increased water quality throughout the system from restoration and 

water quality improvement projects.136

 

Burkholder, J.M., D.A. Tomasko, and B.W. Touchette. 2007. Seagrasses and eutrophication. Journal of 

Experimental Marine Biology and Ecology 350:46-72.

Waycott, M., C.M. Duarte, T.J.B. Carruthers, R.J. Orth, W.C. Dennison, S. Olyarnik, A. Calladine, J.W. 

Fourqurean, K.L. Heck, Jr., A.R. Hughes, G.A. Kendrick, W.J. Kenworthy, F.T. Short, and S.L. Williams. 

2009. Accelerating loss of seagrasses across the globe threatens coastal ecosystems. Proceedings of the 

National Academy of Sciences of the United States of America 106(30):12377-12381.

Short, F.T., B. Polidoro, S.R. Livingstone, K.E. Carpenter, S. Bandeira, J.S. Bujang, H.P. Calumpong, 

T.J.B. Carruthers, R.G. Coles, W.C. Dennison, P.L.A. Erftemeijer, M.D. Fortes, A.S. Freeman, T.G.

Jagtap, A.H.M. Kamal, G.A. Kendrick, W.J. Kenworthy, Y.A. La Nafie, I.M. Nasution, R.J. Orth, A. 

Prathep, J.C. Sanciangco, B. van Tussenbroek, S.G. Vergara, M. Waycott, and J.C. Zieman. 2011. 

Extinction risk assessment of the world’s seagrass species. Biological Conservation144:1963-1971.

Watson R.A., R.G. Coles, and W.J. Lee Long. 1993. Simulation estimates of annual yield and landed value 

for commercial penaeid prawns from a tropical seagrass habitat, Northern Queensland, Australia. 

Australian Journal of Marine and Freshwater Research 44:211–219.

Carlson, P., and L. Yarbro. 2008. Seagrass Mapping and Monitoring: Big Bend and Beyond. Presented at 

Florida Water Resources Monitoring Council Meeting, St. Petersburg, FL, September 24-25, 2008.

Costanza, R., R. d’Arge, R. de Groot, S. Farber, M. Grasso, B. Hannon, K. Limburg, S. Naeem, R.V. Neill, 

J. Paruelo, R.G. Raskin, P. Sutton, and M. van den Belt. 1997. The value of the world’s ecosystem services 

and natural capital. Nature 387:253–260. 135 FDEP. 2011. Celebrate Seagrass Awareness Month. Florida Department of Environmental Protection. 

<http://www.dep.state.fl.us/coastal/news/articles/2011/1103_Seagrass.htm>. Accessed June 2011.

Scott, R. 2011. Seagrass Awareness Month. Proclamation by Governor Rick Scott of the State of Florida. 

Florida Department of Environmental Protection. 

<http://www.dep.state.fl.us/coastal/habitats/seagrass/awareness/Proclamation_2011.pdf>. Accessed June 

2011.

136 USEPA. 2009. Determining an Estuary’s Economic Value. EPA-842F09001. U.S. Environmental 

Protection Agency, National Estuary Program, Washington, DC. 

<http://water.epa.gov/type/oceb/nep/upload/2009_05_28_estuaries_inaction_Efficient_IndianRiver.pdf>. 

Accessed July 2011.
Page 54 of 221

According to a study on the impacts of HABs on beachfront tourism-dependent 

businesses in the Ft. Walton Beach and Destin areas of Florida, HABs reduced restaurant 

and lodging revenues by $2.8 million and $3.7 million per month, respectively, 

representing a 29 percent to 35 percent decline in average monthly revenues.137

A study by Mather Economics estimated the effects of water quality on real estate 

value in the South Florida Water Management District. The aggregate owner-occupied 

residential real estate value in the 16-county South Florida Water Management District is 

approximately $976 billion. If water quality (measured by dissolved oxygen levels) can 

be returned to 1970 levels as a result of restoring the Everglades (a potential 23.4 percent 

improvement in water quality), the study found that real estate values would increase by

$16 billion.138

In addition to negatively impacting Florida businesses, nitrogen and phosphorus 

pollution increases costs for beach cleanup, HAB monitoring, and wastewater treatment. 

For example, approximately $63,000 was spent annually from 1995-1997 to dispose of 

red seaweed and fish killed by HAB events that littered 17.5 miles of beach in Sarasota 

County.139

In addition, there are increased costs due to the need to treat polluted sources of 

drinking water. As an example of increased costs for drinking water treatment, in 1991, 

Des Moines (Iowa) Water Works constructed a $4 million ion exchange facility to 

 137 Larkin, S.L., and C.M. Adams. 2007. Harmful algal blooms and coastal business: economic 

consequences in Florida. Society & Natural Resources 20(9):849-859. 138 McCormick, B., R. Clement, D. Fischer, M. Lindsay, R. Watson. 2010. Measuring the Economic 

Benefits of America’s Everglades Restoration: An Economic Evaluation of Ecosystem Services Affiliated 

with the World’s Largest Ecosystem Restoration Project. Prepared for the Everglades Foundation, Palmetto 

Bay, FL, by Mather Economics, Roswell, GA. 139 Hoagland, P., D.M. Anderson, Y. Kaoru, and A.W. White. 2002. The economic effects of harmful algal 

blooms in the United States: estimates, assessment issues, and information needs. Estuaries 25:819-837.
Page 55 of 221

remove nitrate from its drinking water supply. This facility was designed to be used an 

average of 35–40 days per year to remove excess nitrate levels at a cost of nearly $3,000 

per day.140 In another example, Fremont, Ohio (a city of approximately 20,000) has 

experienced high levels of nitrate from its drinking water source, the Sandusky River, 

resulting in numerous drinking water use advisories. An estimated $15 million is needed 

to build a reservoir (and associated piping) that will allow for selective withdrawal from 

the river to avoid elevated levels of nitrate and provide storage.141 By regulating 

allowable levels of chlorophyll a in Oklahoma drinking water reservoirs, the Oklahoma 

Water Resources Board estimated that the long-term cost savings in averted drinking 

water treatment for 86 systems would range between $106 million and $615 million if 

such regulations were implemented.142 These statistics are illustrative of what treatment 

to address nitrates and nitrites can cost. Any impacts in Florida would be site-specific and 

might or might not be comparable to these numbers.

B. Statutory and Regulatory Background 

Section 303(c) of the CWA (33 U.S.C. 1313(c)) directs states to adopt WQS for 

their navigable waters. CWA Section 303(c)(2)(A) and EPA's implementing regulations 

at 40 CFR 131 require, among other things, that state WQS include the designated use 

and criteria that protect those uses. EPA regulations at 40 CFR 131.11(a)(1) provide that 

states shall “adopt those water quality criteria that protect the designated use” and that 

 140 Jones, C.S., D. Hill, and G. Brand. 2007. Use a multifaceted approach to manage high sourcewater 

nitrate. Opflow June:20–22. 141 Taft, Jim, Association of State Drinking Water Administrators (ASDWA). 2009. Personal 

Communication. 

142 Moershel, Philip, Oklahoma Water Resources Board (OWRB) and Mark Derischweiler, Oklahoma 

Department of Environmental Quality (ODEQ). 2009. Personal Communication.

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such criteria “must be based on sound scientific rationale and must contain sufficient 

parameters or constituents to protect the designated use.” In addition, 40 CFR 131.10(b) 

provides that "[i]n designating uses of a water body and the appropriate criteria for those 

uses, the state shall take into consideration the water quality standards of downstream 

waters and ensure that its water quality standards provide for the attainment and 

maintenance of the water quality standards of downstream waters.” 

States are also required to review their water quality standards at least once every 

three years and, if appropriate, revise or adopt new standards (CWA section 303(c)(1)). 

Any new or revised water quality standards must be submitted to EPA for review and 

approval or disapproval (CWA section 303(c)(2)(A) and (c)(3)). In addition, CWA 

section 303(c)(4)(B) authorizes the Administrator to determine, even in the absence of a 

state submission, that a new or revised standard is needed to meet CWA requirements. 

The EPA approved the State of Florida’s rules (which include criteria for certain estuaries 

and coastal marine waters) on November 30, 2012. The criteria proposed in this 

rulemaking protect the uses designated by the State of Florida and implement Florida’s 

narrative nutrient provision at Subsection 62-302.530(47)(b), F.A.C. for the purposes of 

the CWA. These criteria include numeric values that apply to Florida’s estuaries and 

coastal waters not covered by the newly-approved State WQS, south Florida inland 

flowing waters, and DPVs to ensure the attainment and maintenance of the water quality 

standards of downstream estuaries.143 As explained more fully in Section I.A, EPA does 

not intend to finalize these DPVs if the district court modifies the Consent Decree 

 143 The criteria proposed in this rulemaking do not address or implement Florida’s narrative nutrient 

provision at Subsection 62-302.530(47)(a), F.A.C. Subsection 62-302.530(47)(a), F.A.C. remains in place 

as an applicable water quality standard for CWA purposes.

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consistent with EPA’s amended determination that numeric DPVs are not necessary to 

meet CWA requirements in Florida.

C. Water Quality Criteria 

Water quality criteria include three components. The first component is 

“magnitude,” the concentration of a pollutant that can be maintained over time in the 

ambient receiving water without adversely affecting the designated use that the criteria is 

intended to support. The second component is “duration,” or the time period over which 

exposure is averaged (i.e., the averaging period) to limit the time of exposure to elevated 

concentrations. This accounts for the variability in the quality of the ambient water due to 

variations of constituent inputs, flow, and other factors. The third component is 

“frequency,” or how often the magnitude/duration condition may be exceeded and still 

protect the designated use. Combining the criterion-magnitude with the duration and 

frequency prevents harmful effects from infrequent exceedances of the criterionmagnitude by ensuring compensating periods of time during which the concentration is 

below the criterion-magnitude. When criterion-magnitudes are exceeded for short periods 

of time or infrequently, aquatic life can typically recover; that is, the designated uses of 

the water body are typically protected. Designated uses are typically not protected when 

criterion-magnitudes are exceeded for longer periods of time (i.e., for longer than the 

specified duration) or more frequently (i.e., more often than the allowed frequency).

144

 144 USEPA. 1994. Water Quality Standards Handbook: Second Edition, Chapter 3 – Water Quality 

Criteria. EPA-823-B-94-005a. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

USEPA 1991. Technical Support Document for Water Quality-based Toxics Control. Appendix D –

Duration and Frequency. EPA/505/2-90-001. U.S. Environmental Protection Agency, Office of Water, 

Washington, DC. 
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Use of this magnitude-duration-frequency format allows for some exceedances of the 

criterion-magnitude concentrations while still protecting applicable designated uses, 

which is important for pollutants such as nitrogen and phosphorus because their 

concentrations can vary naturally in the environment.

Under CWA section 304(a), EPA periodically publishes criteria 

recommendations for use by states in setting water quality criteria for particular 

parameters to protect recreational and aquatic life uses of waters. Where EPA has 

published recommended criteria, states have the option of adopting water quality criteria 

based on EPA’s CWA section 304(a) criteria guidance, section 304(a) criteria guidance 

modified to reflect site-specific conditions, or other scientifically defensible methods (40 

CFR 131.11(b)(1)). 

For nitrogen and phosphorus pollution, EPA has published under CWA section 

304(a) a series of peer-reviewed, national technical approaches and methods for the 

development of numeric nutrient criteria for lakes and reservoirs,145 rivers and streams,146

and estuarine and coastal marine waters.147 EPA based the methodologies used to 

develop numeric nutrient criteria for Florida in this proposed regulation on these 

published guidance documents, which identify three scientifically defensible approaches 

for deriving nutrient criteria: (1) the reference condition approach derives criteria from 

observations collected in reference water bodies or during reference time periods; (2) the 

mechanistic modeling approach represents contaminant loadings, hydrodynamics, and 

 145 USEPA. 2000a. Nutrient Criteria Technical Guidance Manual: Lakes and Reservoirs. EPA-822-B-00-

001. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

146 USEPA. 2000b. Nutrient Criteria Technical Guidance Manual: Rivers and Streams. EPA-822-B-00-

002. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

147 USEPA. 2001. Nutrient Criteria Technical Manual: Estuarine and Coastal Marine Waters. EPA-822-B01-003. U.S. Environmental Protection Agency, Office of Water, Washington, DC.
Page 59 of 221

impacts in aquatic systems using equations that represent physical and ecological 

processes, calibrated using site-specific data; and (3) the stressor-response approach

estimates the relationship between nutrient concentrations and response measures related 

to a designated use of the water body. These three analytical approaches have been 

independently peer-reviewed and are appropriate for deriving scientifically defensible 

numeric nutrient criteria, taking into consideration the method-specific data needs and 

available data. In addition to these approaches, consideration of established (e.g., 

published and peer-reviewed) nutrient response thresholds is also an acceptable approach 

for deriving criteria.148

The criteria proposed in this rulemaking implement Florida’s narrative nutrient 

provision at Subsection 62-302.530(47)(b), F.A.C., for the purposes of the CWA as

numeric values that apply to, and protect, Class I, II, and III estuaries and coastal waters 

in Florida and south Florida inland flowing waters. In Florida, water quality criteria 

established for Class I, II, and III surface waters must protect “fish consumption, 

recreation and the propagation and maintenance of a healthy, well-balanced population of 

fish and wildlife.”149 Florida’s existing narrative nutrient provision serves to protect Class 

I, II, and III waters from nitrogen and phosphorus pollution by requiring that “[i]n no 

case shall nutrient concentration of a body of water be altered so as to cause an imbalance 

in natural populations of aquatic flora or fauna.” 

After an extensive review of the latest scientific knowledge relating to the impacts 

of nutrient pollution on aquatic systems, EPA is proposing the use of three biological 

 148 USEPA. 2000a. Nutrient Criteria Technical Guidance Manual: Lakes and Reservoirs. EPA-822-B-00-

001. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

149 Pursuant to Subsection 62-302.400(4), F.A.C.
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endpoints – maintenance of seagrasses, maintenance of balanced algal populations, and 

maintenance of aquatic life (fauna) – as the most sensitive to effectively derive numeric 

nutrient criteria that will protect Class I, II, and III designated uses from the harmful, 

adverse effects of nutrient pollution. The endpoint measures that EPA is proposing to use 

to determine the nutrient concentrations to protect these biological endpoints are light 

levels to maintain historic depth of seagrass colonization, chlorophyll a concentrations 

associated with balanced phytoplankton biomass, and sufficient DO to maintain aquatic 

life. Fish consumption relies on the presence of fish and aquatic life as well as the habitat 

that supports them, which in turn relies on seagrasses and limited occurrence of nuisance 

algal blooms. The protection of recreation (both fishing and swimming related uses) 

relies on the presence of fish and aquatic life as well as limited occurrence of nuisance 

algal blooms. Lastly, the protection of propagation and maintenance of a healthy, wellbalanced population of fish and wildlife relies on the presence of fish and aquatic life as 

well as the habitat that supports them. 

EPA's January 14, 2009 determination addressed Florida’s narrative nutrient 

provision at Subsection 62-302.530(47)(b), F.A.C. As discussed earlier, EPA has 

proposed and promulgated criteria, in this and other proposals, to implement that 

provision, which provides that "[i]n no case shall nutrient concentrations of a body of 

water be altered so as to cause an imbalance in natural populations of aquatic flora or 

fauna. The criteria proposed in this rulemaking do not address or implement Florida’s 

narrative nutrient provision at Subsection 62-302.530(47)(a), F.A.C. which provides that 

“[t]he discharge of nutrients shall continue to be limited as needed to prevent violations 

of other standards contained in this chapter. Human-induced nutrient enrichment (total 

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nitrogen or total phosphorus) shall be considered degradation in relation to the provisions 

of Sections 62-302.300, 62-302.700, and 62-4.242, F.A.C.” Subsection 62-

302.530(47)(a), F.A.C. remains in place as an applicable WQS for CWA purposes and 

could result in more stringent nitrogen and phosphorus limits than those proposed in this 

rule, where necessary to protect other applicable water quality standards in Florida. 

D. EPA Determination Regarding Florida and Consent Decree

On January 14, 2009, EPA determined under CWA section 303(c)(4)(B) that new 

or revised water quality standards in the form of numeric water quality criteria for 

nitrogen and phosphorus pollution are necessary to meet the requirements of the CWA in 

the State of Florida. EPA’s determination is available at the following website:

http://water.epa.gov/lawsregs/rulesregs/florida_consent.cfm. 

Subsequently, EPA entered into a Consent Decree with Florida Wildlife 

Federation, Sierra Club, Conservancy of Southwest Florida, Environmental 

Confederation of Southwest Florida, and St. Johns Riverkeeper, effective on December 

30, 2009, which established a schedule for EPA to propose and promulgate numeric

nutrient criteria for Florida’s lakes, springs, flowing waters, estuaries, and coastal waters, 

as well as downstream protection values (DPVs) to protect downstream lakes and 

estuaries. The Consent Decree provided that if Florida submitted and EPA approved 

numeric nutrient criteria for the relevant water bodies before the dates outlined in the 

schedule, EPA would no longer be obligated to propose or promulgate criteria for those 

water bodies.

E. EPA’s Rulemaking and Subsequent Litigation

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Page 62 of 221

On December 6, 2010, EPA published a rule finalizing numeric nutrient criteria 

for Florida’s lakes, springs, and flowing waters outside of the South Florida Nutrient 

Watershed Region (40 CFR 131.43). The 2010 “inland waters rule” was previously 

scheduled to take effect on March 6, 2012, with the exception of one provision that 

allowed entities to submit Site-Specific Alternative Criteria (SSAC) effective February 4, 

2011. The March 6, 2012 effective date was subsequently extended on two occasions (77 

FR 13497 and 77 FR 39949) such that the current effective date of the rule is January 6, 

2013. Concurrently with this proposal, EPA is issuing a separate proposed rule to stay the 

inland waters rule until November 15, 2013. For more information on the proposed stay 

rule, see http://water.epa.gov/lawsregs/rulesregs/florida_inland.cfm.

Following the publication of the inland waters rule, 12 cases were filed in the U.S. 

District Court for the Northern District of Florida challenging the rule. The cases, 

consolidated before Judge Robert Hinkle in the Tallahassee Division of the Northern 

District, were filed by environmental groups, Florida’s State Department of Agriculture, 

the South Florida Water Management District, and various industry/discharger groups. 

The challenges alleged that EPA’s determination and final inland waters rule were 

arbitrary, capricious, an abuse of discretion, and not in accordance with the law for a 

variety of reasons. Oral argument in the case was held on January 9, 2012 before Judge 

Hinkle.

On February 18, 2012, the Court upheld EPA’s January 2009 determination and 

the final numeric nutrient criteria for Florida’s lakes and springs, as well as the sitespecific alternative criteria (SSAC) provisions and the provisions for calculating DPVs 
Page 63 of 221

using either modeling or a default option for an impaired lake that is not attaining its 

numeric nutrient criteria.150 With regard to EPA’s numeric nutrient criteria for flowing 

waters (i.e., streams) and the default option to calculate DPVs for unimpaired lakes based 

on ambient stream nutrient concentrations at the point of entry to the lake, the Court 

found that EPA had not provided sufficient information in its final rule explaining why or 

how the criteria or DPV protect against harmful increases, as opposed to any increase, in 

nutrients. The Court observed that EPA’s scientific approach to deriving stream criteria 

(i.e., the reference condition approach), including the criteria’s duration and frequency 

components, “are matters of scientific judgment on which the rule would survive 

arbitrary-or-capricious review.” The Court also found, however, that EPA had not 

explained in sufficient detail how the stream criteria would prevent a “harmful increase in 

a nutrient level”. In addition, the Court found that EPA had not explained in sufficient 

detail how exceedances of the default DPV for unimpaired lakes would lead to “harmful 

effects” in the downstream lake. Thus, the Court invalidated these two aspects of EPA’s 

final rule and remanded them to the Agency for further action. Concurrently with this 

proposal, EPA is issuing a separate proposed rule for Florida’s streams and DPVs for 

unimpaired lakes (Water Quality Standards for the State of Florida’s Streams and 

Downstream Protection Values for Lakes: Remanded Provisions). For more information 

on the proposed rule for the remanded provisions, see 

http://water.epa.gov/lawsregs/rulesregs/florida_inland.cfm.

 150 Case 4:08-cv-00324-RH-WCS, February 18, 2012.
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On several occasions, the court granted EPA’s request to modify the deadlines in 

the December 2009 Consent Decree.151 Under the revised Consent Decree, EPA is 

required to propose criteria for Florida’s estuaries, coastal waters, and south Florida 

inland flowing waters by November 30, 2012 and to finalize such criteria by September 

30, 2013. 

In accordance with the January 14, 2009 determination, the December 30, 2009 

Consent Decree, and the subsequent modifications to the deadlines in the December 30, 

2009 Consent Decree, EPA is proposing in this notice numeric nutrient criteria for 

estuaries and coastal waters in the State of Florida, and south Florida inland flowing 

waters. This proposed rule satisfies EPA’s requirement to propose criteria for these three 

categories of Florida waters by November 30, 2012.

F. Florida Adoption of Numeric Nutrient Criteria and EPA Approval

On June 13, 2012, FDEP submitted new and revised WQS for review by the EPA 

pursuant to section 303(c) of the CWA. These new and revised WQS are set out primarily 

in Rule 62-302 of the F.A.C. [Surface Water Quality Standards]. FDEP also submitted 

amendments to Rule 62-303, F.A.C. [Identification of Impaired Surface Waters], which 

sets out Florida’s methodology for assessing whether waters are attaining State WQS. On 

November 30, 2012, EPA approved the provisions of these rules submitted for review 

that constitute new or revised WQS (referred to in this preamble as the “newly-approved 

State WQS”). 

 151 http://water.epa.gov/lawsregs/rulesregs/florida_consent.cfm
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Among the newly-approved State WQS are numeric criteria for nutrients that 

apply to a set of estuaries and coastal marine waters in Florida. Specifically, these newlyapproved State WQS apply to Clearwater Harbor/St. Joseph Sound, Tampa Bay, Sarasota 

Bay, Charlotte Harbor/Estero Bay, Clam Bay, Tidal Cocohatchee River/Ten Thousand 

Islands, Florida Bay, Florida Keys, and Biscayne Bay. Under the Consent Decree, EPA is 

relieved of its obligation to propose numeric criteria for these waters.

III. Proposed Numeric Criteria for Florida’s Estuaries, Coastal Waters, and South 

Florida Inland Flowing Waters 

In this notice of proposed rulemaking, EPA is proposing numeric nutrient criteria 

to protect against harmful increases in nutrients, and therefore, protect the designated 

uses of the State of Florida’s Class I, II, and III waters, specifically Florida’s estuaries 

and coastal waters (excluding those contained in Florida’s newly-approved State WQS), 

and south Florida inland flowing waters. This proposed rule also includes downstream 

protection values (DPVs) to ensure the attainment and maintenance of WQS in

downstream estuarine and south Florida marine waters. The proposed criteria and related 

provisions in this rule reflect a detailed consideration of the best available scientific 

research, data, and analyses related to the specific circumstances for deriving numeric 

nutrient criteria in the State of Florida. EPA’s actions are consistent with and support 

existing Florida WQS regulations. 
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EPA proposes developing numeric nutrient criteria to restore and maintain the 

balance of natural populations of aquatic flora and fauna in Florida waters. The analytical 

process that EPA used to derive the proposed criteria consisted of several steps that 

included (1) classification of the water body systems, (2) subdividing water body systems 

into smaller segments that have similar chemical, physical, and biological features, (3) 

review and analysis of biological endpoints, and (4) application of one or more analytical 

methodologies.

After accounting for the spatial coverage of Florida’s newly-approved State 

WQS, EPA grouped Florida’s remaining estuarine and coastal waters according to the 

natural geographic features of estuarine basins and their associated watersheds

(classification). This resulted in 19 estuarine systems and three coastal systems. Next, 

EPA divided each resulting estuary and coastal system into segments on the basis of 

similar biological, chemical, and physical attributes (segmentation). Segmentation 

resulted in 89 estuarine segments among the 19 estuarine systems and 71 coastal 

segments among the three coastal systems. In the Big Bend region (Ochlockonee Bay to 

Springs Coast) EPA combined coastal waters with estuarine waters for analysis. The 

classification serves as an organizing framework for analyses, and the segmentation 

delineates areas in each estuary or coastal system where the numeric nutrient criteria 

apply.

EPA is proposing to develop numeric nutrient criteria for Florida’s estuarine and 

coastal waters based on three biological endpoints that are sensitive to changes in 

nitrogen and phosphorus concentrations. These biological endpoints reflect the water 

quality conditions necessary to ensure protection of balanced populations of aquatic flora 
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and fauna: (1) maintenance of seagrasses (as measured by water clarity sufficient to 

maintain historic depth of seagrass colonization), (2) maintenance of balanced algal 

populations (as measured by chlorophyll a concentrations associated with balanced 

phytoplankton biomass), and (3) maintenance of aquatic life (as measured by levels of 

dissolved oxygen sufficient to maintain aquatic life). For each water body, EPA derived 

numeric nutrient criteria based on the most nutrient sensitive of the three endpoints and 

the sufficiency of data available in each segment. 

For each estuary and coastal system, one of three analytical approaches was used 

to derive numeric nutrient criteria—reference condition, stressor-response (statistical 

modeling), and mechanistic modeling. In some cases, a secondary approach provided

corroborating evidence for the results of the primary analytical methodology. EPA 

evaluated multiple lines of evidence to determine the analytical approach that was best 

suited for derivation of numeric nutrient criteria in each estuarine or coastal system. In 

general, and as discussed in more detail in later Sections of this proposed rule, the 

reference condition approach was applied when there were sufficient data available to 

characterize conditions that were representative of and protective of designated uses, the 

stressor-response approach was applied when there were sufficient data available to 

statistically quantify relationships between nutrient concentrations and the biological 

endpoints, and lastly, the mechanistic modeling approach was applied when there were 

sufficient data and information available to quantify the relationships between nutrient 

loads and the biological endpoints.

For calculating DPVs for estuaries and south Florida marine waters, EPA is 

proposing four approaches for setting nitrogen and phosphorus protective levels in a 
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hierarchy that reflects the data and scientific information available, including (1) water 

quality simulation modeling, (2) reference condition approach, (3) dilution models, and 

(4) the numeric nutrient criteria in the estuarine segment to which a freshwater stream or 

canal discharges.

For south Florida EPA is proposing the use of downstream protection values 

(DPVs) to manage nitrogen and phosphorus pollution in the inland flowing waters and 

protect the water quality of estuaries and coastal waters downstream. As in estuarine and 

coastal systems, EPA followed a series of steps to derive criteria in south Florida inland 

flowing waters, including classification of water bodies, segmentation, review and 

analysis of biological endpoints, application of analytical methodologies, and 

development of DPVs. EPA defined south Florida inland flowing waters as inland 

predominantly fresh surface waters that have been classified as Class I or Class III, which 

encompasses the waters south of Lake Okeechobee, the Caloosahatchee River (including 

Estero Bay) watershed, and the St. Lucie watershed. EPA segmented south Florida waters 

by identifying 22 canal pour points that drain freshwater to each marine segment. To 

manage nitrogen and phosphorus pollution in the inland flowing waters and protect the 

water quality of estuaries and coastal waters downstream EPA then screened water 

quality data at each pour point to prevent the use of upstream water quality data that 

coincided with a documented downstream impact. EPA then calculated DPVs using the 

reference condition approach.

In deriving scientifically sound numeric nutrient criteria for this proposed 

rulemaking, EPA relied on the local technical expertise of various scientific experts in 

Florida. EPA met and consulted with FDEP’s scientific and technical experts during the 
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development of these numeric nutrient criteria as part of an ongoing collaborative process 

to analyze, evaluate, and interpret a substantial amount of Florida-specific data. EPA 

carefully evaluated the technical approaches and scientific analyses that FDEP presented 

as part of their draft approaches to develop numeric nutrient criteria for estuaries within 

the State. Finally, EPA also carefully considered substantial stakeholder input from 

twelve public hearings conducted by FDEP during 2010, in addition to working with 

scientists from several Florida National Estuary Programs (NEPs), Water Management 

Districts, universities, and other government agencies in Florida.

To further ensure the best use of available data and scientific analyses for deriving 

criteria, the Agency submitted its potential methods and approaches for an independent, 

scientific peer review by EPA’s Science Advisory Board (SAB) in November 2010. The 

SAB reviewed the document entitled, Methods and Approaches for Numeric Nutrient 

Criteria for Nitrogen/Phosphorus Pollution in Florida’s Estuaries, Coastal Waters, and 

Southern Inland Flowing Waters, and submitted their final recommendations to EPA in 

July 2011.152 The SAB agreed that a dual nutrient strategy to derive criteria for both 

nitrogen and phosphorus is warranted. The SAB also found that all of the approaches that 

EPA proposed for use in this rulemaking (i.e., reference condition, stressor-response, and 

mechanistic modeling) have utility and recommended that a combination of approaches 

be used where data and models are available. The SAB provided numerous 

recommendations to strengthen the application of the approaches to develop numeric 

 152 USEPA-SAB. 2011. Review of EPA’s Draft Approaches for Deriving Numeric Nutrient Criteria for

Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. EPA-SAB-11-010. U.S. 

Environmental Protection Agency, Science Advisory Board, Washington, DC.

USEPA. 2010. Methods and Approaches for Deriving Numeric Criteria for Nitrogen/Phosphorus Pollution 

in Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. U.S. Environmental 

Protection Agency, Office of Water, Washington, DC.
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nutrient criteria for Florida waters that EPA has used to refine the methods and 

approaches for deriving the criteria proposed in this rulemaking.

153

Section III.A provides an overview of the technical elements used to support 

derivation of the numeric nutrient criteria proposed in this rulemaking for estuaries and 

coastal waters.

154 The remainder of Section III specifically describes EPA’s proposed 

numeric nutrient criteria for estuaries (Section III.B), coastal waters (Section III.C), and 

south Florida inland flowing waters (Section III.D). Also included are proposed DPVs for 

estuaries (Section III.B) and south Florida marine waters (Section III.D). 

A. General Information and Approaches

For each group of waters addressed in Section III, EPA is proposing to use 

system-specific approaches based on the classification and segmentation results for each 

system (described in detail in Sections III.B, III.C, and III.D) for the derivation of 

numeric nutrient criteria to ensure that the diversity of unique ecosystems found in each 

type of water body is taken into consideration. This system-specific approach allows the 

Agency to consider the physical, chemical, and biological characteristics of a particular 

water body and to select a scientifically defensible approach, considering the data and 

information available for each system. This section describes the technical approaches 

EPA employed to derive the proposed criteria and DPVs, including (1) data and 

segmentation, (2) biological endpoints, and (3) analytical methodologies. 

1. Data Sources and Segmentation

 153EPA response letter to SAB. 

<http://yosemite.epa.gov/sab/sabproduct.nsf/fedrgstr_activites/DCC3488B67473BDA852578D20058F3C9

/$File/EPA-SAB-11-010_Response_10-26-2011.pdf>. Accessed May 2012. 154 Additional details are provided in a separate document, the Technical Support Document for U.S. EPA’s 

Proposed Rule for Numeric Nutrient Criteria for Florida’s Estuaries, Coastal Waters, and Southern Inland 

Flowing Waters (TSD); located at www.regulations.gov, Docket ID No. EPA-HQ-OW-2010-0222.
Page 71 of 221

a) Estuaries

Florida’s estuarine areas encompass approximately 1,950 square miles. EPA used 

the IWR Run 40 database155 to identify available data from a range of sampling sites in 

Florida’s estuaries. To compute relationships between nutrient concentrations and 

chlorophyll a, EPA relied on measurements of Total Kjeldahl Nitrogen (TKN), TN, 

Nitrate-Nitrite (NO3-NO2), TP, and chlorophyll a from the IWR Run 40 database. The 

resulting dataset included 180,814 water quality samples, collected at 13,648 sites. The 

Agency also analyzed additional data submitted by local experts and organizations. 

The water quality and biological communities of an estuary are affected by 

multiple factors related to the shape and size of the estuary, its connections to the ocean, 

geology, climate, and watershed characteristics (e.g., watershed area and land use). 

Because each of these factors can vary from one system to another, causing the water 

quality and aquatic populations of flora and fauna in each estuary to be distinct, EPA 

proposes to classify 19 individual estuarine systems based on the natural geographic 

features of estuarine basins and their associated watersheds. This approach has been 

utilized previously in development of the NOAA Coastal Assessment Framework.156

This approach is also consistent with a watershed approach to water quality management, 

which EPA encourages as a way to integrate and coordinate efforts within a watershed in 

order to most effectively and efficiently assess conditions and implement controls.157

 155 Florida's IWR data are the chemical, physical and biological water quality data that FDEP uses to create 

its integrated reports. IWR Run 40. Updated through February 2010. FL IWR and STORET can be found 

at: <http://www.dep.state.fl.us/WATER/STORET/INDEX.HTM> 156 NOAA. 2007. NOAA’s Coastal Geospatial Data Project, Coastal Assessment Framework (CAF). 

NOAA/NOS Special Projects Office - Coastal Geospatial Data Project. Silver Spring, MD. 

<http://coastalgeospatial.noaa.gov/>. Accessed May 2012. 157 USEPA. 2008. Handbook for Developing Watershed Plans to Restore and Protect Our Waters. EPA 

841-B-08-002. U.S. Environmental Protection Agency, Office of Water, Washington DC.
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EPA is proposing to sub-divide each estuarine system into segments based on 

physical factors and long-term average salinity gradients. Estuaries are complex and 

dynamic systems that reflect the mixing of fresh and marine water, and different 

ecological zones correspond to differences in salinity within each estuary. The estuary 

segments are expected to have unique physical, chemical, and biological characteristics 

that may respond differently to nutrient inputs than other segments within the same 

estuary.

158 EPA is proposing numeric nutrient criteria for 89 individual segments in 19

estuaries. A detailed description and detailed maps of EPA’s proposed within-estuary 

segments are provided in the TSD (Volume 1: Estuaries, Section 1.3 and for each 

estuarine system in Section 2).

b) Coastal Waters

There are substantial data available from satellite remote sensing that can be used 

in a scientifically defensible and reliable way in conjunction with available field 

monitoring data to derive numeric chlorophyll a criteria for coastal waters. Satellite 

remote sensing technologies have been widely used159 to measure chlorophyll a in 

approximately 3,865 square miles of coastal waters in Florida. These technologies allow 

consistent and reliable monitoring of expansive areas of Florida's coastline. 

The data EPA used to derive numeric chlorophyll a criteria for Florida’s coastal 

waters encompass a twelve year period of record (1998-2009). The length of this data 

record captures the long-term variability that has been observed in water quality within 

Florida’s coastal waters and allows EPA to take advantage of the available remote 

 158 Telesh, I.V., and V.V. Khlebovich. 2010. Principal processes within the estuarine salinity gradient: A 

review. Marine Pollution Bulletin 61(4-6):149-155. 159 Gregg, W.W., and N.W. Casey. 2004. Global and regional evaluation of the SeaWiFS chlorophyll data 

set. Remote Sensing of Environment 93(4):463-479.
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sensing data. To obtain chlorophyll a measurements from satellite remote sensing (chlRSa), EPA processed data from over 1,000 8-day composites of remotely sensed images 

from satellite ocean color data. The eight-day binning period is a standard approach based 

on the satellite orbit repeat period of 16 days for the Sea-viewing Wide Field-of-view 

Sensor (SeaWiFS) satellite.160 EPA also obtained field monitoring TN, TP, and 

chlorophyll a data from FDEP IWR Run 40, the Northeastern Gulf of Mexico Chemical 

Oceanography and Hydrography Study (NEGOM), the Ecology and Oceanography of 

Harmful Algal Blooms Research Program (ECOHAB), the Florida Fish and Wildlife 

Conservation Commission Fish and Wildlife Research Institute (FWRI), NOAA 

Oceanographic Data Center (NODC), Mote Marine Laboratory, and the SeaWiFS Biooptical Archive and Storage System (SeaBASS). Field monitoring data included over 

5,500 chlorophyll a measurements, which were reduced to 1,947 measurements after 

screening for data quality, as described later in this proposed rule.

EPA is not proposing to derive TN and TP criteria for Florida’s coastal waters due 

to lack of sufficient field monitoring data for TN and TP. Although it would be a more 

reliable indicator to include TN and TP in combination with chlorophyll a, EPA believes 

that the chlorophyll a criteria should protect these Florida waters because chlorophyll a

can be a sensitive biological parameter that would serve as a signal to the State that 

nutrient pollution is creating an imbalance in the natural populations of aquatic flora and 

fauna in Florida's coastal waters. Where EPA has not derived criteria for certain 

parameters in this proposed rule, due to insufficient scientific evidence to support a 

 160 Campbell, J.W., J.M. Blaisdell, and M. Darzi. 1995. Volume 32, Level-3 SeaWiFS Data Products: 

Spatial and Temporal Binning Algorithms. In: SeaWiFS Technical Report Series. eds. Hooker, S.B., E.R. 

Firestone, and J.G. Acker. NASA Technical Memorandum 104566, Vol. 32. National Aeronautics and 

Space Administration. Greenbelt, MD. 
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protective threshold for numeric nutrient criteria (e.g., TN and TP for the majority of 

Florida’s coastal waters), EPA or the State may consider deriving criteria in the future for 

those parameters.

To ensure data quality, EPA screened available field monitoring data to find 

samples with, at a minimum, metadata for date, time, latitude, longitude, and chlorophyll 

a or light attenuation information. Where multiple samples of chlorophyll a at different 

depths existed, EPA selected the sample closest to the surface in order to provide a better 

comparison to the remotely sensed data. The monitoring sampling times were also

compared to the satellite overpass times. EPA used samples falling within a plus or minus

three hour time window to minimize variability between the sample time and satellite 

overpass time. EPA then compared the satellite chlRS-a data to the field monitored 

chlorophyll a data. From this assessment EPA determined that chlRS-a accurately 

represents chlorophyll a in coastal waters.

For the purposes of deriving criteria for coastal waters using remote sensing data, 

EPA is proposing to exclude chlRS-a measurements taken during known bloom events of 

Karenia brevis from the statistical distribution of coastal data. K. brevis is a 

dinoflagellate responsible for red tide. Satellites can detect K. brevis blooms when cell 

counts are above 50,000 cells/L. EPA flagged coastal segments with cell counts greater 

than 50,000 cells/L during an 8-day composite and did not include them in the chlRS-a

distributions used in criteria derivation.

161 In addition, the same segment was flagged one 

week prior to and after a bloom detection to provide a temporal buffer as blooms are 

transported along the coast. This proposed approach is consistent with recommendations 

 161 Heil, C.A., and K.A. Steidinger. 2009. Monitoring, management, and mitigation of Karenia blooms in 

the Eastern Gulf of Mexico. Harmful Algae 8:611-617.
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from the Agency’s Science Advisory Board, which recommended EPA screen out these 

data points, as they are likely not representative of reference conditions.

162 Analyses of 

cumulative distributions of chlRS-a show they are minimally affected by inclusion or 

removal of observations affected by K. brevis. 

EPA classified Florida’s coastal waters into three main areas: the Florida 

Panhandle, West Florida Shelf, and Atlantic Coast. These three coastal areas were 

subdivided into a total of 71 segments based on FDEP’s Water Body Identification 

System (WBIDs), physical factors, the optical properties of the coastal areas, water 

quality characteristics, and the jurisdictional limits of the Clean Water Act (i.e., three 

nautical mile seaward limit). A detailed description of EPA’s data screening process and 

a map of the coastal waters are provided in the TSD (Volume 2: Coastal Waters, Section

1.3).

c) Request for Comment on Data and Segmentation

EPA believes the proposed data and segmentation approaches provide a strong 

foundation for the derivation of numeric nutrient criteria that will protect the designated 

uses in Florida's estuaries and coastal waters. EPA requests comment on all aspects of 

these approaches. Additionally, the Agency is soliciting additional relevant data and 

information to assist in the derivation of numeric nutrient criteria. Relevant data and 

information includes, but is not limited to: monitoring data for DO, chlorophyll a, TN, 

TP, TKN, dissolved organic nitrogen, dissolved organic phosphorus, dissolved inorganic 

 162 USEPA-SAB. 2011. Review of EPA’s draft Approaches for Deriving Numeric Nutrient Criteria for

Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. EPA-SAB-11-010. U.S. 

Environmental Protection Agency, Science Advisory Board, Washington, DC.
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nitrogen, dissolved inorganic phosphorus, and NO3-NO2. EPA also invites comment on 

the timeframe of the data used to derive criteria for each of the water body types. In 

addition, EPA requests comment on excluding chlRS-a measurements taken during known 

bloom events of K. brevis from the statistical distribution of coastal data. EPA also 

solicits additional available scientific data and information that could be used in the 

derivation of numeric criteria for nitrogen and phosphorus in coastal waters.

Even though waters were assigned to segments to ensure homogeneity of water 

quality across different locations within a segment, EPA recognizes that limited 

variability may still exist across locations within a given segment. EPA also solicits 

comment on and requests any additional available information regarding the ability of the 

proposed segmentation approaches to account for the unique water quality conditions that 

can be found in estuarine and coastal waters throughout the State. Finally, EPA is 

proposing to derive numeric nutrient criteria using a system-specific approach. EPA 

requests comment on the spatial scale of the proposed criteria and whether a broader 

spatial approach would be more appropriate.

2. Biological Endpoints

When deriving numeric nutrient criteria, it is important to identify nutrientsensitive biological endpoints relevant to particular estuarine and coastal systems. These 

biological endpoints serve as sensitive measures to identify protective concentrations of 

TN, TP, and chlorophyll a that, in turn, will support balanced natural populations of 

aquatic flora and fauna and protect the State’s designated uses. EPA conducted an 

extensive evaluation of available scientific literature to select appropriate biological 
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endpoints, reviewing over 800 documents. From this review of the latest scientific 

knowledge, EPA has determined that maintenance of seagrasses, maintenance of 

balanced algal populations, and maintenance of aquatic life are three sensitive biological 

endpoints, which can be measured by water clarity (as it relates to light levels sufficient 

to maintain historic depth of seagrass colonization), chlorophyll a, and DO, respectively, 

and appropriately used in derivation of numeric nutrient criteria that protect the State’s 

designated uses from harmful increases in nitrogen and phosphorus concentrations. The 

selection of these biological endpoints was based upon their scientific defensibility;

sensitivity to harmful, adverse effects caused by the pollutants nitrogen and phosphorus;

and the sufficiency of data available for each.

EPA derived TN, TP, and chlorophyll a criteria to: (1) maintain water clarity to 

achieve seagrass depth of colonization targets, (2) reduce the risk of phytoplankton 

blooms, and (3) maintain dissolved oxygen concentrations sufficient for balanced, natural 

aquatic life in Florida’s estuaries and coastal waters. As set out more fully in the 

following discussion, these three biological endpoints provide a scientifically defensible 

basis upon which to derive numeric nutrient criteria that protect balanced natural 

populations of aquatic flora and fauna over the full range of estuarine and coastal 

conditions across Florida; waters that achieve these endpoints support designated uses.

a) Maintenance of Seagrasses 

EPA selected the maintenance of seagrasses, as measured by water clarity to 

maintain historic depth of seagrass colonization, as one biological endpoint and 

corresponding endpoint measure to derive numeric nutrient criteria for estuaries. Healthy 

populations of seagrasses serve as widely recognized indicators of biological integrity in
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estuarine systems and, in turn, of balanced natural populations of aquatic flora and 

fauna.163

Because of the unique conditions that are created within seagrass communities, 

populations of other aquatic floral and faunal species benefit from the presence and 

abundance of seagrasses.164 For example, seagrasses act as nurseries for many species by 

providing refuge from predators. Seagrasses also improve water quality by trapping 

suspended sediments, preventing sediment resuspension, and retaining nutrients. 

Florida’s NEPs and FDEP have also used endpoints based on seagrasses to derive their 

recommended estuarine criteria because of seagrass sensitivity to nutrient pollution.

Seagrass communities depend on a variety of physical, chemical, and biological 

conditions to thrive. Among these, adequate underwater light availability (as measured by 

water clarity) is one critical factor for seagrass health. The relationship between water 

clarity and the depth to which seagrasses grow, known as the depth of colonization, has 

been well-documented.165 When seagrasses receive sufficient sunlight, seagrass biomass 

 163 Ferdie, M., and J.W. Fourqurean. 2004. Responses of seagrass communities to fertilization along a 

gradient of relative availability of nitrogen and phosphorus in a carbonate environment. Limnology and 

Oceanography 49(6):2082-2094.

Orth, R.J., T.J.B. Carruthers, W.C. Dennison, C.M. Duarte, J.W. Fourqurean, K.L. Heck, A.R. Hughes, 

G.A. Kendrick, W.J. Kenworthy, S. Olyarnik, F.T. Short, M. Waycott, and S.L. Williams. 2006. A global 

crisis for seagrass ecosystems. BioScience 56(12):987-996.

Doren, R.F., J.C. Trexler, A.D. Gottlieb, and M.C. Harwell. 2009. Ecological indicators for system-wide 

assessment of the greater everglades ecosystem restoration program. Ecological Indicators 9:S2-S16.

Gibson, G.R., M.L. Bowman, J. Gerritsen, and B.D. Snyder. 2000. Estuarine and Coastal Marine Waters: 

Bioassessment and Biocriteria Technical Guidance. EPA 822-B-00-024. U.S. Environmental Protection 

Agency, Office of Water, Washington, DC. 

http://water.epa.gov/scitech/swguidance/standards/criteria/aqlife/biocriteria/upload/2009_04_22_biocriteria

_States_estuaries_estuaries.pdf. . Accessed November 2011. 164 Orth, R.J., T.J.B. Carruthers, W.C. Dennison, C.M. Duarte, J.W. Fourqurean, K.L. Heck Jr., A.R. 

Hughes, G.A. Kendrick, W.J. Kenworthy, S. Olyarnik, F.T. Short, M. Waycott, and S.L. Williams. 2006. A 

global crisis for seagrass ecosystems. Bioscience 56(12):987-996. 165 Dennison, W.C. 1987. Effects of light on seagrass photosynthesis, growth, and depth distribution. 

Aquatic Botany 27:15-26.

Dennison, W.C., R.J. Orth, K.A. Moore, J.C. Stevenson, V. Carter, S. Kollar, P.W. Bergstrom, and R.A. 

Batiuk. 1993. Assessing water quality with submersed aquatic vegetation. BioScience 43(2):86-94.
Page 79 of 221

remains constant or increases over time. Conversely, when incoming light is blocked by 

substances in the water column, such as phytoplankton, suspended solids, or color, 

seagrass growth slows or stops. Studies on seagrasses have documented the relationship 

of nutrient pollution-related accelerated algal growth to declines in available light and 

subsequent declines in seagrass communities.166 Since the area within an estuary 

available for seagrass growth is partially a function of the total area with enough sunlight 

at sufficient depths to sustain growth, as water clarity decreases and reduces the amount 

of sunlight that can reach the seagrasses, the available area for seagrass growth also 

decreases. Hence, the greater the water clarity (and associated available light), the deeper 

the water that can support seagrass communities and, therefore, the greater the extent of 

seagrass coverage. 

EPA reviewed studies that empirically assessed the relationship between seagrass

growth and available light167 and is proposing that, for Florida, when an average value of 

 

Duarte, C.M. 1991. Seagrass depth limits. Aquatic Botany 40(4):363-377.

Gallegos, C.L. 1994. Refining habitat requirements of submersed aquatic vegetation: Role of optical 

models. Estuaries 17(1):187-199.

Gallegos, C.L., and W.J. Kenworthy. 1996. Seagrass depth limits in the Indian River Lagoon (Florida, 

USA): Application of an optical water quality model. Estuarine, Coastal and Shelf Science 42(3):267-288.

Gallegos, C.L. 2005. Optical water quality of a blackwater river estuary: the Lower St. Johns River, 

Florida, USA. Estuarine, Coastal and Shelf Science 63(1-2):57-72.

Steward, J.S., R.W. Virnstein, L.J. Morris, and E.F. Lowe. 2005. Setting seagrass depth, coverage, and light 

targets for the Indian River Lagoon system, Florida. Estuaries and Coasts 28(6):923-935. 166 Ferdie, M., and J.W. Fourqurean. 2004. Responses of seagrass communities to fertilization along a 

gradient of relative availability of nitrogen and phosphorus in a carbonate environment. Limnology and 

Oceanography 49(6):2082-2094. 

Orth, R.J., T.J.B. Carruthers, W.C. Dennison, C.M. Duarte, J.W. Fourqurean, K.L. Heck, A.R. Hughes, 

G.A. Kendrick, W.J. Kenworthy, S. Olyarnik, F.T. Short, M. Waycott, and S.L. Williams. 2006. A global 

crisis for seagrass ecosystems. BioScience 56(12):987-996. 167 Dennison, W.C., R.J. Orth, K.A. Moore, J.C. Stevenson, V. Carter, S. Kollar, P.W. Bergstrom, and R.A. 

Batiuk. 1993. Assessing water quality with submersed aquatic vegetation. BioScience 43(2):86-94.

Duarte, C.M. 1991. Seagrass depth limits. Aquatic Botany 40(4):363-377.

Gallegos, C.L. 1994. Refining habitat requirements of submersed aquatic vegetation: Role of optical 

models. Estuaries 17(1):187-199.

Steward, J.S., R.W. Virnstein, L.J. Morris, and E.F. Lowe. 2005. Setting seagrass depth, coverage, and light 

targets for the Indian River Lagoon system, Florida. Estuaries and Coasts 28(6):923-935.
Page 80 of 221

20 percent of the sunlight that strikes the water’s surface (incident light) reaches the 

bottom of the water column (to the depth of seagrass colonization), sufficient light is 

available to maintain seagrasses. A similar value has been used in previous nutrient 

management efforts in Florida.168

EPA is also proposing that protecting and maintaining water clarity sufficient to 

support an appropriate depth of colonization provides the greatest protection of balanced

natural populations of aquatic flora and fauna since maintenance of seagrass habitat is 

critical to ecosystem conditions. EPA used available historical seagrass coverage data 

(including the earliest available, generally 1940-1960, or more recent, 1992) to compute 

the historical maximum depth of seagrass colonization as a reference. In all cases the 

most recent (2000-2010) seagrass coverage was also evaluated to determine existing 

depth of colonization, and to relate this value to existing water quality. To compute 

seagrass depth of colonization, EPA overlaid seagrass coverage data and bathymetric data 

compiled by NOAA using a Geographic Information System.169 EPA then used the data 

on seagrass coverage to determine the maximum depths that seagrasses have been able to 

grow in each estuary, where applicable (this approach was not used in some estuaries in 

Florida that do not have historical evidence of seagrass colonization), in order to identify 

a reference point for a healthy level of seagrass colonization. Because seagrass habitats 

support a rich array of biological uses,170 EPA is proposing to derive numeric nutrient 

 168 Janicki, A.J., and D.L. Wade. 1996. Estimating critical external nitrogen loads for the Tampa Bay 

estuary: an empirically based approach to setting management targets. Technical Publication 06-96.

Prepared for Tampa Bay National Estuary Program, St. Petersburg, FL, by Coastal Environmental, Inc., St. 

Petersburg, FL.

170 Hughes, A.R., S.L. Williams, C.M. Duarte, K.L. Heck, Jr., and M. Waycott. 2009. Associations of 

concern: declining seagrasses and threatened dependent species. Frontiers in Ecology and the Environment

7(5):242-246.
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criteria to maintain a comparable depth of seagrass colonization to the reference level 

(i.e. seagrasses growing at the deepest observed depth of colonization) to ensure 

protection of balanced natural populations of aquatic flora and fauna. EPA chose to use 

the historical maximum observed depth, and resulting areal coverage, because increasing 

nutrients beyond the point that is protective of maximum coverage of seagrass is likely to 

cause a decline in seagrass coverage. Because a wide variety of organisms rely on healthy 

seagrass communities, a decrease in seagrass coverage to levels below the maximum 

observed depth will result in a decline in overall system health and biodiversity.171 EPA 

calculated a water clarity target that would ensure 20% percent of incident light at the 

surface would be able to reach the reference depth of colonization. Finally, EPA used this 

water clarity target to derive numeric criteria for TN, TP, and chlorophyll a to support 

balanced natural populations of aquatic flora and fauna. (More detail on the importance 

of seagrass can be found in the TSD, Volume 1: Estuaries, Section 1.2.1).

b) Maintenance of Balanced Algal Populations 

Based upon EPA’s extensive review of current scientific literature, EPA selected 

maintenance of balanced algal populations, as measured by the chlorophyll a

concentrations associated with balanced phytoplankton biomass, as the second biological 

endpoint and corresponding endpoint measure to derive numeric nutrient criteria for

estuaries and coastal waters. The maintenance of balanced algal populations is an 

 171 Hughes, A.R., S.L. Williams, C.M. Duarte, K.L. Heck, Jr., and M. Waycott. 2009. Associations of 

concern: declining seagrasses and threatened dependent species. Frontiers in Ecology and the Environment

7(5):242-246.

Orth, R.J., T.J.B. Carruthers, W.C. Dennison, C.M. Duarte, J.W. Fourqurean, K.L. Heck, A.R. Hughes, 

G.A. Kendrick, W.J. Kenworthy, S. Olyarnik, F.T. Short, M. Waycott, and S.L. Williams. 2006. A global 

crisis for seagrass ecosystems. BioScience 56(12):987-996.

FFWCC. 2003. Conserving Florida's Seagrass Resources: Developing a Coordinated Statewide 

Management Program. Florida Fish and Wildlife Conservation Commission, Florida Marine Research 

Institute. St. Petersburg, FL.
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important sensitive biological endpoint because of its responsiveness to nutrient 

enrichment, integral role in aquatic food webs, well-established use as an integrative 

measure of aquatic ecosystem condition, and correlation with changes in floral 

composition and subsequent faunal response.172 Chlorophyll a is the endpoint measure of 

balanced algal populations, and has a long history of use in aquatic ecology as a measure 

of phytoplankton biomass and production.173 Elevated chlorophyll a concentrations 

resulting from nutrient pollution-enhanced algal growth and accumulation are a welldocumented symptom of eutrophication and the harmful, adverse impacts of nitrogen and 

phosphorus pollution across the nation, and specifically in Florida (refer to Section II.A 

for additional information).174 In most of Florida’s coastal and estuarine waters, healthy 

biological communities depend on balanced natural populations of algae because algae

are integral components of aquatic food webs and aquatic nutrient cycling.175

 172 Boyer, J.N., C.R. Kelble, P.B. Ortner, and D.T. Rudnick. 2009. Phytoplankton bloom status: 

Chlorophyll a biomass as an indicator of water quality condition in the southern estuaries of Florida, USA. 

Ecological Indicators 9s:S56-S67.

Hagy, J.D., J.C. Kurtz, and R.M. Greene. 2008. An approach for developing numeric nutrient criteria for a 

Gulf coast estuary. EPA 600R-08/004. U.S. Environmental Protection Agency, Office of Research and 

Development, National Health and Environmental Effects Research Laboratory, Gulf Breeze, FL.

Bricker, S.B., C.G. Clement, D.E. Pirhalla, S.P. Orlando, and D.R.G. Farrow. 1999. National Estuarine 

Eutrophication Assessment. Effects of Nutrient Enrichment in the Nation’s Estuaries. National Oceanic and 

Atmospheric Administration, National Ocean Service, Special Projects Office and the National Centers for 

Coastal Ocean Science, Silver Spring, MD.

See Section B.3 in Appendix B of USEPA. 2010. Methods and Approaches for Deriving Numeric Criteria 

for Nitrogen/Phosphorus Pollution in Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing 

Waters. U.S. Environmental Protection Agency, Office of Water, Washington, DC. 173 Wetzel, R.G. 2001. Limnology: Lakes and River Ecosystems. 3rd ed. Academic Press, San Diego, CA.

Kalff, J. 2002. Limnology: Inland Water Ecosystems. Prentice-Hall, Inc., Upper Saddle River, New Jersey. 174 Elser, J.J., M.E.S. Bracken, E.E. Cleland, D.S. Gruner, W.S. Harpole, H. Hillebrand, J.T. Ngai, E.W. 

Seabloom, J.B. Shurin, and J.E. Smith. 2007. Global analysis of nitrogen and phosphorus limitation of 

primary production in freshwater, marine, and terrestrial ecosystems. Ecology Letters 10:1135-1142.

Smith, V.H. 2006. Responses of estuarine and coastal marine phytoplankton to nitrogen and phosphorus 

enrichment. Limnology and Oceanography 51(1 part 2):377–384 175 Hauxwell, J., C. Jacoby, T. Frazer, and J. Stevely. 2001. Nutrients and Florida’s Coastal Waters: The 

Links Between People, Increased Nutrients and Changes to Coastal Aquatic Systems. Florida Sea Grant 

Report No. SGEB-55. Florida Sea Grant College Program, University of Florida, Gainesville, FL.

<http://edis.ifas.ufl.edu/pdffiles/SG/SG06100.pdf>. Accessed June 2011.
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Elevated chlorophyll a concentrations resulting from nitrogen and phosphorus

pollution alter the trophic state of estuarine and coastal waters and increase the frequency 

and magnitude of algal blooms. EPA evaluated the available scientific literature to 

determine chlorophyll a concentrations indicative of phytoplankton blooms associated 

with imbalance in natural populations of aquatic flora and fauna. Published reports on 

chlorophyll a concentrations in estuarine waters across the nation, including Florida 

estuaries, reflect the range of natural trophic states and enrichment. These studies suggest

that low algal bloom conditions are defined as maximum chlorophyll a concentrations 

less than or equal to 5 μg/L, medium bloom conditions are defined as maximum 

chlorophyll a concentrations from greater than 5 to 20 μg/L, high bloom conditions are 

defined as maximum chlorophyll a concentrations from greater than 20 to 60 μg/L, and 

hypereutrophic conditions are defined by maximum bloom concentrations above 60 

μg/L.

176 Two Florida estuaries, Florida Bay and Pensacola Bay, were analyzed as a part 

of a larger NOAA national survey of estuaries. The authors reported the average 

chlorophyll a concentrations were 20 μg/L or less for seven of ten large estuaries

nationally, and were especially low for Florida Bay (8 μg/L) and Pensacola Bay (10 

μg/L).177 Other literature regarding phytoplankton blooms indicated similar results.178

 

NOAA. 2011. Overview of Harmful Algal Blooms. National Oceanic and Atmospheric Administration, 

Center for Sponsored Coastal Research. 

<http://www.cop.noaa.gov/stressors/extremeevents/hab/default.aspx>. Accessed June 2011. 176 Bricker, S.B., J.G. Ferreira, and T. Simas. 2003. An integrated methodology for assessment of estuarine 

trophic status. Ecological Modelling 169(1):39-60. 177 Glibert, P.M., C.J. Madden, W. Boynton, D. Flemer, C. Heil, and J. Sharp, eds. 2010. Nutrients in 

Estuaries: A Summary Report of the National Estuarine Experts Workgroup, 2005–2007. Report to U.S. 

Environmental Protection Agency, Office of Water, Washington DC.

178 OECD. 1982. Eutrophication of Waters: Monitoring, Assessment and Control. Organisation for 

Economic Cooperation and Development, Paris, France.

Painting, S.J., M.J. Devlin, S.J. Malcolm, E.R. Parker, D.K. Mills, C. Mills, P. Tett, A. Wither, J. Burt, R. 

Jones, and K. Winpenny. 2007. Assessing the impact of nutrient enrichment in estuaries: susceptibility to 

eutrophication. Marine Pollution Bulletin 55:74–90.
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Chlorophyll a concentrations associated with hypereutrophic conditions (>60 

μg/L) reflect a trophic state that is unnatural for Florida estuaries. While some estuaries 

in the State are more productive than others, high chlorophyll a concentrations (20 to 60 

μg/L) also do not appear to reflect balanced conditions in Florida, especially given 

observed ranges in Florida. Concentrations of chlorophyll a in this high range are 

associated more frequently with loss of seagrass and a shift of algal populations to 

monoculture or, in other words, a loss in the balance of diverse populations of aquatic 

flora.

179 Moreover, this concentration range was also associated with conditions where 

other uses, including recreation, are adversely affected. Based on the range of chlorophyll 

a concentrations indicative of natural algal bloom conditions characteristic of Florida 

estuaries, as well as the literature on concentrations associated with harmful, adverse 

conditions for estuarine biota and other use support, EPA is proposing a chlorophyll a

concentration of 20 μg/L as the water quality target to define a nuisance algal bloom. 

Thus, estuarine waters with chlorophyll a concentrations that exceed this water quality 

target threshold are indicative of imbalanced populations of aquatic flora and fauna

(More detail regarding EPA’s analysis can be found in the TSD, Volume 1: Estuaries, 

Section 1.2.2).

EPA also considered the available scientific research described in this section to

establish an allowable frequency of occurrence of phytoplankton blooms, represented by 

 

Painting, S.J., M.J. Devlin, S.I. Rogers, D.K. Mills, E.R. Parker, and H.L. Rees. 2005. Assessing the 

suitability of OSPAR EcoQOs for eutrophication vs. ICES criteria for England and Wales. Marine 

Pollution Bulletin 50:1569–1584.

Tett, P., R. Gowen, D. Mills, T. Fernandes, L. Gilpin, M. Huxham, K. Kennington, P. Read, M. Service, M. 

Wilkinson, and S. Malcolm. 2007. Defining and detecting undesirable disturbance in the context of marine 

eutrophication. Marine Pollution Bulletin 55:282–297. 179 Bricker, S.B., J.G. Ferreira, and T. Simas. 2003. An integrated methodology for assessment of estuarine 

trophic status. Ecological Modelling 169(1):39-60.
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chlorophyll a levels greater than 20 μg/L, to further define this endpoint measure. EPA is 

proposing a value of 10% as an allowable frequency of occurrence of phytoplankton 

blooms, that is, chlorophyll a measurements may not exceed 20 μg/L more than 10% of 

the time. This frequency is also consistent with current nutrient management practices in 

Florida, such as those utilized in approved Florida TMDLs. 

c) Maintenance of Aquatic Life 

EPA selected maintenance of aquatic life, as measured by the sufficiency of 

dissolved oxygen (DO) to maintain aquatic life, as a third biological endpoint and 

corresponding endpoint measure to derive numeric nutrient criteria for estuaries. DO 

concentrations are a well-known indicator of the health of estuarine and coastal biological 

communities. Aquatic animals including fish, benthic macroinvertebrates, and 

zooplankton depend on adequate levels of DO to survive and grow. These levels may 

differ depending on the species and life stage of the organism (e.g., larval, juvenile, and 

adult).180

To derive the DO endpoint, EPA conducted an analysis of the dissolved oxygen 

requirements of sensitive species in Florida using the Virginian Province dissolved 

oxygen evaluation procedure.181 This analysis derives DO levels that protect both larval 

recruitment and growth for aquatic organisms. EPA used the results of this analysis to 

determine the dissolved oxygen water quality targets considered for numeric nutrient 

 180 Diaz, R.J. 2001. Overview of hypoxia around the world. Journal of Environmental Quality 30(2):275-

281.

Diaz, R.J., and R. Rosenberg. 2008. Spreading dead zones and consequences for marine ecosystems. 

Science 321(5891):926-929. 181 Vincent, A.M., J. Flippin, E. Leppo, and J.D. Hagy III. Dissolved oxygen requirements of Floridaresident saltwater species applied to water quality criteria development. In review.

USEPA. 2000. Ambient Aquatic Life Water Quality Criteria for Dissolved Oxygen (Saltwater): Cape Cod 

to Cape Hatteras. EPA-822-R-00-012. U.S. Environmental Protection Agency, Office of Water, 

Washington DC. 
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criteria development that would protect sensitive aquatic species in Florida estuaries. 

EPA is proposing that satisfying three different DO requirements in Florida’s estuarine 

waters would meet the needs of resident sensitive aquatic species, and thus support the 

maintenance of aquatic life. These requirements are an instantaneous DO concentration 

of 4.0 mg/L, a daily average DO concentration of 5.0 mg/L, and a bottom water average 

DO concentration of 1.5 mg/L. Both the instantaneous minimum of 4.0 mg/L and the 

daily average of 5.0 mg/L are spatial averages over the water column for each estuarine 

segment. These values and interpretations are consistent with existing Florida DO criteria 

(Subsection 62-302.530(30), F.A.C.) and FDEP’s assessment procedures (Subsection 62-

303.320(5), F.A.C.). (More detail on both the existing Florida DO criteria and EPA’s

analysis can be found in the TSD, Volume 1: Estuaries, Sections 1.2.3 and 1.4.1). 

d) Other Endpoints Considered by EPA

EPA considered, but is not proposing to use, the following nutrient-sensitive 

biological endpoints: (1) harmful algal blooms (HABs), (2) coral, (3) epiphytes, (4) 

macroinvertebrate and fish indices, (5) macroalgae, (6) Spartina marshes (salt-marshes), 

and (7) the Eastern oyster (Crassostrea virginica). EPA did not select these biological 

endpoints because there was an absence of sufficient data to quantify the link between 

measurements of these endpoints and nitrogen and phosphorus concentrations. Additional 

details on these alternative endpoints are provided in Appendix B in the Methods and 

Approaches for Deriving Numeric Criteria for Nitrogen/Phosphorus Pollution in 

Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters.

182

 182 USEPA. 2010. Methods and Approaches for Deriving Numeric Criteria for Nitrogen/Phosphorus 

Pollution in Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. U.S. 

Environmental Protection Agency, Office of Water, Washington, DC.
Page 87 of 221

e) Request for Comment on Endpoints

EPA believes that maintenance of seagrasses, maintenance of balanced algal 

populations, and maintenance of aquatic life are the three most appropriate nutrientsensitive biological endpoints to use to derive numeric nutrient criteria to ensure that 

nutrient concentrations in a body of water protect balanced natural populations of aquatic 

flora and fauna, and in turn support designated uses. EPA requests comment regarding 

the biological endpoints and endpoint measures selected. EPA also solicits additional 

scientific information on other appropriate endpoints that can be used to protect fish 

consumption, recreation, and the propagation and maintenance of a healthy, wellbalanced population of fish and wildlife in Florida’s Class II and III estuarine and coastal 

waters. 

3. Analytical Methodologies

EPA used three analytical approaches to derive TN, TP, and chlorophyll a

numeric nutrient criteria for different types of waters in Florida. In most of Florida 

coastal waters, EPA is proposing to use a reference condition approach that utilizes data 

from waters that support balanced natural populations of aquatic flora and fauna to derive 

numeric nutrient criteria. In Florida estuaries (including some coastal waters in the Big 

Bend Coastal region), EPA is proposing to use statistical and mechanistic models to 

determine protective concentrations of TN, TP, and chlorophyll a linked to biological 

endpoints. Where sufficient data were not available to apply statistical models (i.e., 

stressor-response approach) in all segments in an estuary, EPA used mechanistic model 

predictions to derive criteria. In these instances, EPA analyzed the available stressor-
Page 88 of 221

response analysis as a second line of evidence, in segments where the data were 

available.

a) Reference Condition Approach

EPA is proposing to use the reference condition approach to derive numeric 

nutrient criteria in coastal waters that support balanced natural populations of aquatic 

flora and fauna. EPA is proposing this approach to derive numeric chlorophyll a criteria 

for Florida’s coastal waters because the scientific data and information available were 

insufficient to establish accurate quantifiable relationships between TN and TP

concentrations and harmful, adverse effects due to the limited TN and TP data available.

Therefore, EPA is proposing to rely upon the reference condition approach to identify 

numeric chlorophyll a criteria concentrations that protect the designated uses, and avoid 

any adverse change in natural populations of aquatic flora or fauna in Florida’s coastal 

waters. 

The reference condition approach, which has been well documented, peer 

reviewed, and developed in a number of different contexts,183 is used to derive numeric 

nutrient criteria that are protective of applicable designated uses by identifying numeric 

 183 USEPA. 2000a. Nutrient Criteria Technical Guidance Manual: Lakes and Reservoirs. EPA-822-B-00-

001. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

USEPA. 2000b. Nutrient Criteria Technical Guidance Manual: Rivers and Streams. EPA-822-B-00-002. 

U.S. Environmental Protection Agency, Office of Water, Washington, DC.

Stoddard, J.L., D.P. Larsen, C.P. Hawkins, R.K. Johnson, and R.H. Norris. 2006. Setting expectations for 

the ecological condition of streams: the concept of reference condition. Ecological Applications 16:1267–

1276.

Herlihy, A.T., S.G. Paulsen, J. Van Sickle, J.L. Stoddard, C.P. Hawkins, L.L. Yuan. 2008. Striving for 

consistency in a national assessment: the challenges of applying a reference-condition approach at a 

continental scale. Journal of the North American Benthological Society 27:860–877.

USEPA. 2001. Nutrient Criteria Technical Manual: Estuarine and Coastal Marine Waters. EPA-822-B01-003. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

USEPA-SAB. 2011. Review of EPA’s draft Approaches for Deriving Numeric Nutrient Criteria for

Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. EPA-SAB-11-010. U.S. 

Environmental Protection Agency, Science Advisory Board, Washington, DC.
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nutrient criteria concentrations occurring in least-disturbed, healthy coastal waters that 

are supporting designated uses.

To derive the proposed numeric nutrient criteria using the reference condition 

approach, EPA first selected reference conditions in Florida’s coastal waters where the 

Agency was confident that designated uses are protected. EPA reviewed available 

monitoring information, peer-reviewed literature, and technical reports to ensure that, 

where applicable, seagrass beds are healthy, DO is adequate for sensitive species, 

phytoplankton biomass is balanced, and that any other information relating to the 

ecosystem indicates that the waters are supporting balanced natural populations of 

aquatic flora and fauna. EPA also removed data during periods of temporary known 

human disturbances (e.g., bridge and roadway construction) where natural populations 

were temporarily affected. Finally, EPA reviewed CWA section 303(d) listings, and 

removed data associated with impairment listings for chlorophyll a, dissolved oxygen, 

and nutrients, as well as data from coastal segments adjacent to CWA section 303(d) 

impaired estuary waters, such that the resulting data would reflect unimpaired conditions.

EPA only removed data from the period of impairment. The result of this rigorous 

analysis was a set of reference waters that, although not pristine, reflected healthy 

conditions that were supporting designated uses, and thus free from harmful, adverse 

effects on natural populations of aquatic flora and fauna due to nutrient pollution. EPA 

has confidence that these reference waters are supporting designated uses and balanced 

natural populations of flora and fauna, and has confidence that if the criteria are attained 

or maintained at the concentrations that are among the highest observed in these waters, 

then designated uses and natural populations of aquatic flora and fauna will be protected 
Page 90 of 221

in coastal waters. Further details regarding data screening can be found in the TSD 

(Volume 2: Coastal Waters, Section 1.4).

After selecting the reference waters, EPA calculated the annual geometric mean 

concentrations of chlorophyll a for each year of the data record and for each segment.184

EPA then calculated a normal distribution based on the annual geometric mean 

chlorophyll a concentrations. From this distribution, which represents the population of 

water quality observations in each segment, EPA selected the 90th percentile as the 

applicable criteria for each segment. EPA selected the 90th percentile as an appropriate 

concentration to specify the criterion-magnitude because the Agency is confident that the 

distribution reflects minimally-impacted, biologically healthy reference conditions, which 

support the State’s Class II and III designated uses. The use of the 90th percentile of 

chlorophyll a is also supported by several eutrophication assessment frameworks in 

Europe and the U.S, such as the Oslo-Paris Commission “Common Procedure”(OSPAR),

Water Framework Directive of the EU, Assessment of Estuarine Trophic Status in the 

US, and the Marine Strategy Framework Directive used by the European Commission, 

which identify the 90th percentile as representative of a chlorophyll a concentration above 

which eutrophication is considered ecologically problematic or where an undesirable 

disturbance to aquatic life and water quality from eutrophication are highly likely to 

appear.

185 For further information on the use of the reference approach see the TSD 

(Volume 2, Coastal Waters, Section 1.5.1).

 184 Geometric means were used for averages in the reference condition, statistical modeling, and 

mechanistic modeling approaches because concentrations were log-normally distributed. 185 OSPAR Commission. 2005. Common Procedure for the Identification of the Eutrophication Status of 

the OSPAR Maritime Area (Reference Number: 2005-3). OSPAR Commission, London.

Ferreira, J.G., J.H. Andersen, A. Borja, S.B. Bricker, J. Camp, M.C. da Silva, E. Garcés, A-S. Heiskanen, 
Page 91 of 221

EPA chose not to select the extreme upper end of the distribution (95th or 100th

percentile). This is because these highest observed annual average concentrations (i.e., 

95th or 100th percentile) have rarely been observed at any reference site and are most 

likely to be heavily influenced by extreme event factors (e.g., hurricanes, droughts). Thus 

these highest observed concentrations could be outliers that are not representative of 

conditions that would typically support designated uses and natural populations of 

aquatic flora and fauna. Therefore, EPA has less confidence that such highest observed 

concentrations would continue to be supportive of designated uses and natural 

populations of aquatic flora and fauna if maintained in all coastal waters at all times. 

Alternatively, the selection of a much lower percentile, such as a representation of 

the central tendency of the distribution (i.e., 50th percentile), would not be appropriate 

because it would imply that half of the conditions observed at reference sites would not 

support designated uses and natural populations of aquatic flora and fauna, when EPA’s 

analysis indicates that they do. By setting the criteria at the 90th percentile of the 

reference condition distribution, EPA believes the designated uses, i.e., natural 

populations of aquatic flora and fauna, will be protected when these concentrations are 

attained for the majority of coastal water segments. For those coastal water segments that 

are shown to accommodate or require higher or lower concentrations, the SSAC 

provision is provided in EPA’s proposed rule as discussed in Section V.C.

 

C. Humborg, L. Ignatiades, C. Lancelot, A. Menesguen, P. Tett, N. Hoepffner, and U. Claussen. 2011. 

Overview of eutrophication indicators to assess environmental status within the European Marine Strategy 

Framework Directive. Estuarine, Coastal and Shelf Science 93(2):117-131.

Bricker, S.B., J.G. Ferreira, and T. Simas. 2003. An integrated methodology for assessment of estuarine 

trophic status. Ecological Modelling 169:39–60.

European Commission. 2003. Common Implementation Strategy for the Water Framework Directive 

(2000/60/EC): Guidance Document No. 5, Transitional and Coastal Waters-Typology, Reference 

Conditions and Classification Systems. European Commission, Working Group 2.4—COAST, Office for 

Official Publications of the European Communities, Luxembourg.
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b) Statistical Modeling

EPA evaluated the data available for each estuary segment in terms of temporal 

and spatial representativeness to establish whether there were sufficient data to use a 

statistical model. Where enough monitoring data in estuaries were available, EPA 

developed statistical models (i.e., stressor-response relationships186) that quantified

relationships between TN, TP, chlorophyll a, and the selected endpoint measures (i.e., 

water clarity to maintain maximum depth of seagrass colonization and chlorophyll a

concentrations associated with balanced phytoplankton biomass). There were not enough 

temporally-resolved DO monitoring data, particularly in pre-dawn hours when dissolved 

oxygen concentrations are typically lower than during that day187, in any of the estuaries 

to permit the use of statistical models to derive criterion values associated with sufficient 

DO to support aquatic life. Where the available endpoints were shown to be sufficiently 

sensitive, EPA used these relationships to calculate TN, TP, and chlorophyll a

concentrations that achieved the selected water quality targets for these endpoints, which

serve as measures of balanced natural populations of aquatic flora and fauna. 

To determine chlorophyll a concentrations supportive of the water clarity depth 

target to achieve the healthy seagrass endpoint in a segment, EPA estimated the 

relationship between annual geometric mean chlorophyll a concentrations and annual 

geometric mean water clarity for each segment. Then, EPA computed the chlorophyll a

criterion as the chlorophyll a concentration that was associated with the water clarity

 186 USEPA. 2010. Using stressor-response relationships to derive numeric nutrient criteria. EPA-820-S10-001.U.S. Environmental Protection Agency, Office of Water, Office of Science and Technology, 

Washington, DC. 187 D’Avanzo, C., and J.N. Kremer. 1994. Diel Oxygen Dynamics and Anoxic Events in an Eutrophic 

Estuary of Waquoit Bay, Massachusetts. Estuaries and Coasts 17(1B):131-139. 
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target. In other words, the chlorophyll a criterion was determined such that the water 

quality target for water clarity was achieved on an annual average basis.

188 In some 

segments, increased annual geometric mean chlorophyll a concentrations were not 

associated with decreased annual geometric mean water clarity, possibly because other 

factors, such as suspended sediment or colored dissolved organic material, more strongly 

affected water clarity.189 In these segments, EPA determined that the water clarity 

endpoint was not sufficiently sensitive to increased chlorophyll a, and therefore, this 

endpoint was not used to derive a chlorophyll a criterion, and associated TN and TP 

criteria in that segment. 

EPA also used stressor-response relationships to derive chlorophyll a criteria to

maintain balanced algal populations. To this end, EPA used logistic regression to 

estimate the relationship between annual geometric mean chlorophyll a concentrations

and the probability of any single chlorophyll a measurement exceeding EPA’s proposed 

water quality target of 20 μg/L during the year. Then, EPA derived a chlorophyll a

criterion from this relationship by selecting the annual geometric mean chlorophyll a

concentration that ensured that any single chlorophyll a measurement would not exceed 

20 μg/L more than 10% of the time. 

After calculating chlorophyll a candidate criteria values necessary to meet the 

water quality targets for the two biological endpoints for which data were available

(maintenance of seagrasses and maintenance of balanced algal populations), in each 

water body segment, EPA selected the more stringent of the two as the proposed criterion 

 188 Dennison, W.C. 1987. Effects of light on seagrass photosynthesis, growth, and depth distribution. 

Aquatic Botany 27:15-26. 189 Gallegos, C.L. 2005. Optical water quality of a blackwater river estuary: the Lower St. Johns River, 

Florida, USA. Estuarine, Coastal and Shelf Science 63(1-2):57-72.
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for that segment to ensure that the proposed chlorophyll a criterion would protect both

endpoints. 

To calculate TN and TP criteria associated with the chlorophyll a criterion, EPA 

estimated the relationship between annual geometric mean TN and TP concentrations and 

annual geometric mean chlorophyll a concentrations for each segment. EPA then used 

these relationships to compute the TN and TP concentrations that were required to 

maintain average chlorophyll a concentrations at the chlorophyll a criterion. In some 

estuary segments, increased TN or TP concentrations were not associated with increased 

chlorophyll a concentrations, possibly because of differences in the proportion of TP or 

TN that was composed of biologically unavailable forms of phosphorus or nitrogen, or 

because of unique physical or hydrological characteristics of the estuary segment.190 In 

these segments, EPA determined that chlorophyll a concentrations were not sufficiently 

sensitive to increases in TN or TP concentrations, and therefore, this approach was not 

used to derive criteria for these segments.

In instances where one of the endpoints was not sufficiently sensitive to increases 

in TN or TP concentrations the relationship of the other endpoint to TN or TP was 

examined. If both endpoints were insensitive to TN or TP, then the statistical models 

were not used to derive candidate criteria for the particular nutrient. 

In a limited number of estuary segments, EPA found that the TN, TP, or 

chlorophyll a concentrations that were associated with achieving the water quality targets 

for the biological endpoints were outside (greater than or less than) the range of TN, TP, 

or chlorophyll a concentrations observed in the available data for the estuary. In other 

 190 USEPA. 2001. Nutrient Criteria Technical Manual: Estuarine and Coastal Marine Waters. EPA-822-B01-003. U.S. Environmental Protection Agency, Office of Water, Washington, DC.
Page 95 of 221

words, in these situations, using statistical models to derive numeric nutrient criteria 

would require EPA to extrapolate the TN, TP, and chlorophyll a relationships beyond the 

range of available data. Because of the uncertainty inherent in conducting such

extrapolations, EPA is proposing instead to set numeric nutrient criteria derived from 

these statistically modeled relationships at the 90th percentile or 10th percentile limit of 

the distribution of available data instead of deriving criteria outside the range of data 

observations.191 For example, if the statistically modeled value for TP associated with 

achieving all water quality targets to meet the biological endpoints in an estuary segment 

was less than the lower limit10th percentile of annual average values of TP observed in 

that segment, EPA is proposing to set the criterion value at the 10th percentile lower limit 

of annual average values of TP. This approach defines criterion values that maintain 

balanced natural populations of aquatic flora and fauna within the limits of available data

and is consistent with EPA’s reasoning for the selection of the 90th percentile when using 

the reference condition approach. EPA requests comment on whether to extrapolate

stressor-response relationships beyond the range of available data. For further 

information on the use of statistical modeling approach, see the TSD (Volume 1: 

Estuaries, Section 1.4.2 and Appendix B).

c) Mechanistic Modeling 

EPA also quantified relationships between nitrogen and phosphorus loads and the 

three biological endpoints using a coupled system of watershed models and estuarine 

hydrodynamic and water quality models. These models simulated the physical, chemical, 

and biological processes in a watershed-estuarine system. EPA first used the watershed 

 191 USEPA. 2010. Using Stressor-response Relationships to Derive Numeric Nutrient Criteria. EPA-820-S10-001. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

Comment [E33]: OMB edits accepted.
Page 96 of 221

models to develop estimates of TN, TP, and freshwater inputs to the estuary. Next, EPA 

used the estuarine hydrodynamic and water quality models to simulate estuarine water 

quality responses to the watershed inputs, including changes in estuarine TN, TP, and 

chlorophyll a concentrations, water clarity, and DO. Then, EPA utilized these models to 

determine concentrations of TN and TP that would protect the most nutrient-sensitive 

biological endpoint to derive the numeric nutrient criteria.

To select the appropriate models, EPA developed an inventory of watershed and 

estuary models that have been applied previously to estuaries in Florida, including 

models developed by FDEP.192 Based on the results of the review, EPA selected the 

Loading Simulation Program in C++ (LSPC) 193 to simulate freshwater flows and nutrient 

loading from watersheds, the Environmental Fluid Dynamics Code (EFDC)194 to

simulate estuarine hydrodynamics, and the Water Quality Analysis Simulation Program 

(WASP)195 to simulate estuarine water quality.196

LSPC can continuously simulate the hydrologic and water quality processes on 

pervious and impervious land surfaces, in streams, and in well-mixed impoundments 

throughout the watershed and can provide daily estimates of stream flow, TN, and TP 

concentrations entering the estuary. In addition, LSPC is publicly available and has been 

 192 Wolfe, S.H. 2007. An Inventory of Hydrodynamic, Water Quality, and Ecosystem Models of Florida 

Coastal and Ocean Waters. Florida Department of Environmental Protection, Tallahassee, Florida. 193 USEPA. 2011. Loading Simulation Program in C++ (LSPC). 

http://www.epa.gov/athens/wwqtsc/html/lspc.html. Accessed December 2011. 194 USEPA. 2011. Environmental Fluid Dynamics Code (EFDC). 

http://www.epa.gov/athens/wwqtsc/html/efdc.html. Accessed December 2011. 195 USEPA. 2011. Water Quality Analysis Simulation Program (WASP). 

http://www.epa.gov/athens/wwqtsc/html/wasp.html. Accessed December 2011. 196 USEPA. 2010. Methods and Approaches for Deriving Numeric Criteria for Nitrogen/Phosphorus 

Pollution in Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. U.S. 

Environmental Protection Agency, Office of Water, Washington, DC.
Page 97 of 221

peer reviewed.197 LSPC has been successfully applied for water quality management 

purposes to many watersheds throughout the southeastern United States and Florida. 

Therefore, EPA is proposing to apply the LSPC model to the watersheds in Florida 

outside of the South Florida Nutrient Watershed Region. 

EFDC and WASP have been applied in conjunction to simulate hydrodynamics 

and water quality (respectively) for many water quality management projects throughout 

the southeastern United States and Florida. EFDC and WASP are also publicly available 

and have undergone peer review.

198 Based on the extensive use of these models for 

similar applications and their acceptance in the scientific community, EPA is proposing 

to use the EFDC and WASP models to derive numeric nutrient criteria for Florida’s

estuaries. 

For estuaries where monitoring data were insufficient to calculate criteria using 

the statistical models, EPA mechanistically modeled the conditions in each system and 

corresponding watershed that occurred from 2002-2009 using all available, screened data.

EPA evaluated data over the historic period of record and is proposing to use 2002 

through 2009 as a representative modeling period because complete, continuous flow and 

water quality data were available. This period also reflects the range of hydrology and 

meteorology observed over the historic period of record across the Florida estuaries.

EPA then used relationships between TN, TP, and biological endpoints 

quantified by the mechanistic models to derive numeric nutrient criteria. That is, EPA 

 197 USEPA-SAB. 2011. Review of EPA’s draft Approaches for Deriving Numeric Nutrient Criteria for

Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. EPA-SAB-11-010. U.S. 

Environmental Protection Agency, Science Advisory Board, Washington, DC.

198 USEPA-SAB. 2011. Review of EPA’s draft Approaches for Deriving Numeric Nutrient Criteria for

Florida’s Estuaries, Coastal Waters, and Southern Inland Flowing Waters. EPA-SAB-11-010. U.S. 

Environmental Protection Agency, Science Advisory Board, Washington, DC.
Page 98 of 221

determined the concentrations of TN and TP that were associated with meeting all 

biological endpoints in each segment. 

Because estuaries differ in their physical, chemical, and hydrological 

characteristics, EPA expected that differences would exist in the degree to which 

different biological endpoints respond to changes in nutrient concentration. For example, 

in certain estuaries, high concentrations of colored dissolved organic material (CDOM) 

occur naturally and reduce water clarity. Because of the influence of CDOM in these 

estuarine systems, changes in TN, TP, and chlorophyll a are not strongly associated with 

changes in water clarity. In these systems, the water clarity endpoint does not appear to 

be sensitive to changes in nutrients, and therefore, the water clarity endpoint does not 

provide useful information for the purposes of deriving numeric nutrient criteria in these

systems. In each estuarine system, EPA used output from mechanistic models and 

available monitoring data to evaluate the sensitivity of each endpoint measure to changes 

in nutrients. This analysis was used to determine which endpoints were most critical to 

determine protective nutrient concentrations. Endpoints that were found to be insensitive 

to changes in nutrient concentrations in a particular estuarine system were not considered 

further in deriving numeric nutrient criteria for a system. Numeric nutrient criteria for 

each system were based on the modeled scenario in which the remaining endpoint

measures were met during the modeled period, calculated as annual geometric means for 

each year during the modeled period. Criteria were calculated using the 90th percentile of 

the annual geometric means from the modeled years for the model scenario meeting all 

appropriate endpoints. EPA selected the 90th percentile to account for natural variability 

in the data to represent the upper bound of conditions supporting designated uses. The 
Page 99 of 221

selection of the 90th percentile is appropriate for the same reasons as when using the 

reference condition approach. For further information on the use of the mechanistic 

modeling approach, see the TSD (Volume 1: Estuaries, Section 1.4.1).

d) Request for Comment on Analytical Methodologies

EPA believes that the three proposed analytical methodologies used in 

combination result in numeric nutrient criteria that are supportive of balanced natural 

populations of aquatic flora and fauna, and thus protect Class II and III estuarine and 

coastal waters in the State of Florida from nutrient pollution. These analytical 

methodologies utilized the latest scientific knowledge, nutrient sensitive endpoints, and 

the best available data. The Agency requests comment on the application of the proposed 

methodologies and whether these methodologies are appropriate to derive criteria 

protective of designated uses in Florida's estuaries and coastal waters. Specifically, EPA 

is soliciting comment and any scientific information on the use of these approaches in 

areas where there may be other factors present in addition to nutrients that may also 

affect the three biological endpoints by attenuating light in similar ways as chlorophyll a

(e.g., colored dissolved organic matter (CDOM) or suspended sediments). EPA is also 

requesting comment on the procedures used to screen data to identify reference 

conditions that are supporting balanced natural populations of aquatic flora and fauna. 

B. Proposed Numeric Criteria for Estuaries

1. Introduction
Page 100 of 221

EPA is proposing to use a system-specific approach to derive numeric nutrient 

criteria for estuaries to ensure that the unique physical, chemical, and biological 

characteristics of each estuarine ecosystem are taken into consideration.

199

2. Proposed Numeric Criteria (Estuaries) 

EPA is proposing numeric TN, TP, and chlorophyll a criteria for 89 discrete 

segments within 19 estuarine systems in Florida (Table III.B-1). These include Class II 

and III waters under Florida law (Section 62-302.400, F.A.C.); EPA did not find any

Class I estuarine waters in Florida. The 19 estuaries include seven systems in the Florida 

Panhandle region, four systems in the Big Bend region, and eight systems along the 

Atlantic coast. Maps showing the locations of these estuarine systems and EPA’s 

proposed within-estuary segments are provided in the TSD (Volume 1: Estuaries, Section 

1.3 and Section 2). 

In some areas a gap may exist between maps used by Florida and EPA to show 

where criteria apply. In areas where a gap exists between EPA's proposed criteria and 

Florida's numeric criteria, EPA proposes that Florida's numeric criteria from the adjacent 

estuary or marine segment apply (see Section 62-302.532, F.A.C. for values). EPA 

proposes that Florida's criteria from the northernmost segment of Clearwater Harbor/St 

Joseph Sound (Subsection 62-302.532(a)1., F.A.C.) apply to the waters between that 

segment and the southernmost segment of EPA's Springs Coast estuary system. EPA 

proposes that Florida’s numeric criteria from the northernmost segment of Biscayne Bay 

 199 USEPA. 2001. Nutrient Criteria Technical Manual: Estuarine and Coastal Marine Waters. EPA-822-

B-01-003. U.S. Environmental Protection Agency, Office of Water, Washington, DC.

Glibert, P.M. ,C.J. Madden, W. Boynton, D. Flemer, C. Heil, and J. Sharp, eds. 2010. Nutrients in 

Estuaries: A Summary Report of the National Estuarine Experts Workgroup, 2005–2007. Report to U.S. 

Environmental Protection Agency, Office of Water, Washington DC. 
Page 101 of 221

(Subsection 62-302.532(h)5., F.A.C.) apply to the waters of the intercoastal waterway 

between that segment and the southernmost segment of EPA’s Lake Worth Lagoon 

estuary system. 

In other areas a gap may exist within estuaries covered by Florida's numeric 

criteria. In these areas, EPA proposes that Florida's criteria from the adjacent estuary or 

marine segment to the south apply to that gap. EPA proposes that Florida's criteria from 

(1) the upper Lemon Bay segment (Subsection 62-302.532(d)2., F.A.C.) apply to the 

segment between the upper Lemon Bay segment and the Dona/Roberts Bay segment 

(Subsection 62-302.532(d)1., F.A.C.), (2) the Tidal Cocohatchee River segment 

(Subsection 62-302.532(e)1., F.A.C.) apply to the waters between the Tidal Cocohatchee 

River segment and the Estero Bay segment (Subsection 62-302.532(d)9., F.A.C.), (3) the 

Clam Bay segment (Subsection 62-302.532(j)., F.A.C.) apply between the Clam Bay 

segment and the Tidal Cocohatchee River segment (Subsection 62-302.532(e)1., F.A.C.), 

and (4) the Naples Bay segment (Subsection 62-302.532(e)4., F.A.C.) apply to the 

segment between the Naples Bay segment and the Clam Bay Segment (Subsection 62-

302.532(j)., F.A.C.). For further information regarding the derivation and protectiveness 

of Florida’s criteria, see http://water.epa.gov/lawsregs/rulesregs/florida_index.cfm.

Table III.B-1. EPA’s Proposed Numeric Criteria for Florida’s Estuaries (in 

geographic order from northwest to northeast)

Proposed Criteria

Perdido Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Upper Perdido Bay 0101 0.59 0.042 5.2

Big Lagoon 0102 0.26 0.019 4.9

Central Perdido Bay 0103 0.47 0.031 5.8
Page 102 of 221

Lower Perdido Bay 0104 0.34 0.023 5.8

Pensacola Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Blackwater Bay 0201 0.53 0.022 3.9

Upper Escambia 

Bay 0202 0.43 0.025 3.7

East Bay 0203 0.50 0.021 4.2

Santa Rosa Sound 0204 0.34 0.018 4.1

Lower Escambia 

Bay 0205 0.44 0.023 4.0

Upper Pensacola 

Bay 0206 0.40 0.021 3.9

Lower Pensacola 

Bay 0207 0.34 0.020 3.6

Santa Rosa Sound 0208 0.33 0.020 3.9

Santa Rosa Sound 0209 0.36 0.020 4.9

Choctawhatchee 

Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Eastern 

Choctawhatchee 

Bay

0301 0.47 0.025 8.1

Central 

Choctawhatchee 

Bay

0302 0.36 0.019 3.8

Western 

Choctawhatchee 

Bay

0303 0.21 0.012 2.4

St. Andrews 

Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

East Bay 0401 0.31 0.014 4.6

St. Andrews Sound 0402 0.14 0.009 2.3

Eastern St. Andrews 

Bay 0403 0.24 0.021 3.9

Western St. 

Andrews Bay 0404 0.19 0.016 3.1

Southern St. 

Andrews Bay 0405 0.15 0.013 2.6

North Bay 1 0406 0.22 0.012 3.7

North Bay 2 0407 0.22 0.014 3.7

North Bay 3 0408 0.21 0.016 3.4

West Bay 0409 0.23 0.022 3.8

St. Joseph Bay SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

St. Joseph Bay 0501 0.25 0.018 3.8
Page 103 of 221

Apalachicola 

Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

St. George Sound 0601 0.53 0.019 3.6

Apalachicola Bay 0602 0.51 0.019 2.7

East Bay 0603 0.76 0.034 1.7

St. Vincent Sound 0605 0.52 0.016 11.9

Apalachicola

Offshore 0606 0.30 0.008 2.3

Alligator 

Harbor

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Alligator Harbor 0701 0.36 0.011 2.8

Alligator Offshore 0702 0.33 0.009 3.1

Alligator Offshore 0703 0.33 0.009 2.9

Ochlockonee

Bay+

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Ochlockonee-St. 

Marks Offshore 0825 0.79 0.033 2.7

Ochlockonee

Offshore 0829 0.47 0.019 1.9

Ochlockonee Bay 0830 0.66 0.037 1.8

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

St. Marks River 

Offshore 0827 0.51 0.022 1.7

St. Marks River 0828 0.55 0.030 1.2

Big Bend/ 

Apalachee Bay+

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Econfina Offshore 0824 0.59 0.028 4.6

Econfina 0832 0.55 0.032 4.4

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Fenholloway 0822 1.15 0.444 1.9

Fenholloway 

Offshore 0823 0.48 0.034 10.3

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

SteinhatcheeFenholloway 

Offshore 

0821 0.40 0.023 4.1

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Steinhatchee River 0819 0.67 0.077 1.0

Steinhatchee 0820 0.34 0.018 3.5
Page 104 of 221

Offshore 

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Steinhatchee 

Offshore 0818 0.39 0.032 4.8

Suwannee 

River+

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Suwannee Offshore 0817 0.78 0.049 5.2

Springs Coast+

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Waccasassa River 

Offshore 0814 0.38 0.019 3.9

Cedar Keys 0815 0.32 0.019 4.1

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Crystal River 0812 0.35 0.013 1.3

Crystal-Homosassa 

Offshore 0813 0.36 0.013 2.1

Homosassa River 0833 0.47 0.032 1.9

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(ug/L)

Chassahowitzka 

River 0810 0.32 0.010 0.7

Chassahowitzka 

River Offshore 0811 0.29 0.009 1.7

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Weeki Wachee 

River 0808 0.32 0.010 1.6

Weeki Wachee 

Offshore 0809 0.30 0.009 2.1

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Pithlachascotee 

River 0806 0.50 0.022 2.4

Pithlachascotee 

Offshore 0807 0.32 0.011 2.5

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Anclote River 0804 0.48 0.037 4.7

Anclote Offshore 0805 0.31 0.011 3.2
Page 105 of 221

Anclote Offshore 

South 0803 0.29 0.008 2.6

Clearwater 

Harbor/ St. 

Joseph Sound

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

See Section 62-302.532(1)(a) F.A.C.

Tampa Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

See Section 62-302.532(1)(b) F.A.C.

Sarasota Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

See Section 62-302.532(1)(c) F.A.C.

Charlotte 

Harbor/Lemon 

Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

See Section 62-302.532(1)(d) F.A.C.

Lake Worth 

Lagoon/

Loxahatchee

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

North Lake Worth 

Lagoon 1201 0.55 0.067 4.7

Central Lake Worth 

Lagoon 1202 0.57 0.089 5.3

South Lake Worth 

Lagoon 1203 0.48 0.034 3.6

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Lower Loxahatchee 1301 0.68 0.028 2.7

Middle Loxahatchee 1302 0.98 0.044 3.9

Upper Loxahatchee 1303 1.25 0.072 3.6

St. Lucie

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Lower St. Lucie 1401 0.58 0.045 5.3
Page 106 of 221

Middle St. Lucie 1402 0.90 0.120 8.4

Upper St. Lucie 1403 1.22 0.197 8.9

Indian River 

Lagoon

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Mosquito Lagoon 1501 1.18 0.078 7.5

Banana River 1502 1.17 0.036 5.7

Upper Indian River 

Lagoon 1503 1.63 0.074 9.2

Upper Central 

Indian River Lagoon 1504 1.33 0.076 9.2

Lower Central 

Indian River Lagoon 1505 1.12 0.117 8.7

Lower Indian River 

Lagoon 1506 0.49 0.037 4.0

Halifax River

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Upper Halifax River 1601 0.75 0.243 9.4

Lower Halifax River 1602 0.63 0.167 9.6

Guana, 

Tolomato, 

Matanzas, 

Pellicer

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Upper GTMP 1701 0.77 0.144 9.5

Lower GTMP 1702 0.53 0.108 6.1

Lower St. Johns 

River

SEGMENT SEGMENT ID TN*

(mg/L) TP* (mg/L) Chl-a*1(μg/L)

Lower St. Johns River 1801 0.75 0.095 2.5

Trout River 1802 1.09 0.108 3.6

Trout River 1803 1.15 0.074 7.7

Nassau River

SEGMENT SEGMENT ID TN*

(mg/L) TP* (mg/L) Chl-a*1

(μg/L)

Lower Nassau 1901 0.33 0.113 3.2

Middle Nassau 1902 0.40 0.120 2.4

Upper Nassau 1903 0.75 0.125 3.4

St. Marys River

SEGMENT SEGMENT ID TN*

(mg/L) TP* (mg/L) Chl-a*1(μg/L)

Lower St. Marys River 2002 0.27 0.045 3.0

Middle St. Marys

River 2003 0.44 0.036 2.7
Page 107 of 221

1 Chlorophyll a is defined as corrected chlorophyll, or the concentration of chlorophyll a remaining after 

the chlorophyll degradation product, phaeophytin a, has been subtracted from the uncorrected chlorophyll a

measurement.

* For a given water body, the annual geometric mean of TN, TP, or chlorophyll a, concentrations shall not 

exceed the applicable criterion concentration more than once in a three-year period. + In these four areas (collectively referred to as the “Big Bend region”), coastal and estuarine waters are 

combined. Criteria for the Big Bend region apply to the coastal and estuarine waters in that region. 

a) Summary of Approaches (Estuaries)

1) Proposed Approach (Estuaries)

In estuaries where sufficient monitoring data were available to statistically 

quantify relationships between TN, TP, chlorophyll a, and biological endpoints, and the 

endpoints available to derive criteria were shown to be sufficiently sensitive (i.e., 

Choctawhatchee Bay; St. Joseph Bay; Suwannee River; Indian River Lagoon; Halifax 

River; and the Guana, Tolomato, Matanzas, and Pellicer (GTMP) estuarine system), 

statistical models were used to derive the proposed numeric nutrient criteria. In three of 

the estuaries, Choctawhatchee Bay, St. Joseph Bay, and Indian River Lagoon, there were 

sufficient available data for water clarity associated with historic depth of seagrasses, and 

chlorophyll a concentrations associated with balanced phytoplankton biomass targets,

and these biological endpoints were sensitive to changes in nutrients in most segments, so 

proposed criteria were derived that were protective of these endpoints. In the Suwannee 

River, the water clarity endpoint was not sensitive to changes in nutrients, so proposed 

criteria were derived that were protective of the chlorophyll a target associated with 

balanced phytoplankton biomass. In the Halifax River and GTMP, seagrass has not been 

historically present, so the proposed criteria were derived that awere protective of the 

chlorophyll a target associated with balanced phytoplankton biomass.

In all other estuaries mechanistic models were used to quantify the relationship 

between nutrient loads and biological endpoints. EPA then used the models to derive 

Comment [E34]: OMB edit accepted.
Page 108 of 221

proposed numeric nutrient criteria that protect the endpoints. For each estuary, the 

endpoints that were shown to be sufficiently sensitive to nutrient changes above nonanthropogenic nutrient levels were used, as described in Section III.A.3.c. The endpoints 

for each of the estuaries where mechanistic models were used to derive criteria are noted 

in the following discussion.

In Perdido Bay, Apalachicola Bay, three segments in Lake Worth 

Lagoon/Loxahatchee (Lake Worth Lagoon, segments 1201, 1202, and 1203), and St. 

Lucie, all three biological endpoints were found to be sensitive to changes to nutrients, 

and so proposed criteria were derived that were protective of historic depth of seagrasses

(water clarity), chlorophyll a concentrations associated with balanced phytoplankton 

biomass, and dissolved oxygen concentrations sufficient to maintain aquatic life.

In St. Andrews Bay, 2 segments in the Springs Coast (Anclote River/Anclote 

Offshore, segments 0804 and 0805) and 3 segments in Lake Worth Lagoon/Loxahatchee 

(Lower, Middle, and Upper Loxahatchee, segments 1301, 1302, and 1303), dissolved 

oxygen concentrations were found to be insensitive to changes in nutrients. Proposed 

criteria were derived that were protective of historic depth of seagrasses (water clarity)

and chlorophyll a concentrations associated with balanced phytoplankton biomass.

In Pensacola Bay, 3 segments in Ochlockonee Bay (Ochlockonee-St. Marks 

Offshore/Ochlockonee Offshore/Ochlockonee Bay, segments 0825, 0829, and 0830), and 

4 segments in Big Bend/Apalachee Bay (Econfina/Econfina Offshore, segments 0824, 

0832; Steinhatchee-Fenholloway Offshore, segment 0821; Steinhatchee Offshore, 

segment 0818), and 1 segment in Springs Coast (Anclote Offshore South, segment 0803),

water clarity was found to be insensitive to changes in nutrients. In Alligator Harbor and
Page 109 of 221

2 segments in Springs Coast (Waccasassa River Offshore/Cedar Keys, segments 0814, 

0815), there was not enough available information to derive seagrass depth targets. As a 

result, the proposed criteria were derived to be protective of water quality targets for 

chlorophyll a concentrations associated with balanced phytoplankton biomass and 

dissolved oxygen concentrations sufficient to maintain aquatic life. 

In 2 segments in Ochlockonee Bay (St. Marks Offshore/St. Marks River,

segments 0827, 0828), 2 segments in Big Bend/Apalachee Bay (Steinhatchee 

River/Steinhatchee Offshore, segments 0819, 0820), and 2 segments in Springs Coast 

(Pithlachascotee River/Pithlachascotee Offshore, segments 0806, 0807), dissolved 

oxygen and water clarity were both found to be insensitive to changes in nutrients. In 2 

segments in Big Bend/Apalachee Bay (Fenholloway/Fenholloway Offshore, segments 

0822, 0823) and 7 segments in Springs Coast (Crystal River/Crystal-Homosassa 

Offshore/Homosassa River, segments 0812, 0813, 0833; Chassahowitzka

River/Chassahowitzka Offshore, segments 0810, 0811; and Weeki Wachee/Weeki 

Wachee Offshore, segments 0808, 0809), dissolved oxygen was found to be insensitive to 

changes in nutrients and there was not enough available information to derive seagrass 

depth targets. In Nassau River and St. Marys River, dissolved oxygen was found to be 

insensitive to changes in nutrients and seagrass has not been historically present. For all

of these estuaries, proposed criteria were derived that were protective of chlorophyll a

concentrations associated with balanced phytoplankton biomass.

In the Lower St. Johns River, seagrass has not been historically present, so 

proposed criteria were derived that were protective of chlorophyll a associated with 

balanced phytoplankton biomass and dissolved oxygen concentrations sufficient to 
Page 110 of 221

maintain aquatic life. For this system, EPA used the dissolved oxygen from the SiteSpecific Alternative Criteria, developed by FDEP and adopted for the marine portion of 

the Lower St. Johns River, as an additional DO endpoint with which to derive the 

proposed criteria to support dissolved oxygen concentrations sufficient to maintain 

aquatic life.

200 This DO criterion, adopted as a water quality standard specific to this 

system, was used as an alternative target to the daily water column average DO 

concentration of 5.0 mg/L. 

EPA considered several alternative approaches for deriving estuarine numeric 

nutrient criteria, including approaches proposed by the St. Johns River Water 

Management District for estuaries within their jurisdiction (Lower St. Johns River, 

Mosquito Lagoon, Tolomato-Matanzas estuary, Halifax River estuary, Indian River 

Lagoon, and Banana River). While some of these approaches segmented Florida’s 

estuaries differently than the segmentation approach EPA is proposing, all the alternative 

approaches used multiple biological endpoints and analytical methods to determine the 

health of each system and derive criteria. EPA solicits comments on the alternative 

approaches described in more detail in the following sections. Additional details on these 

approaches are provided in the TSD (Volume 1: Estuaries, Section 2).

2) Alternative for St. Johns River Water Management District Waters

The St. Johns River Water Management District (SJRWMD) submitted proposed 

approaches to EPA for several estuaries within their jurisdiction. These included the St. 

Johns River, Mosquito Lagoon, Tolomato-Matanzas estuary, Halifax River estuary, 

 200 FDEP. 2006. Site Specific Alternative Dissolved Oxygen Criterion to Protect Aquatic Life in the Marine Portions of 

the Lower St. Johns River Technical Support Document. Appendix L In: FDEP. 2008. TMDL Report: Total Maximum 

Daily Load for Nutrients for the Lower St. Johns River. Florida Department of Environmental Protection, Tallahassee, 

FL.
Page 111 of 221

Indian River Lagoon, and Banana River. In general, SJRWMD proposed a weight of 

evidence approach employing several analytical techniques to derive numeric nutrient 

criteria for each of the systems. The following paragraphs outline the methods proposed 

for each of these systems.

The SJRWMD has proposed the use of the values for TN, TP, and chlorophyll a

for the Lower St. Johns River (LSJR) that have already been developed as part of an 

existing TMDL to support designated uses in the river. The LSJR is defined as the main 

stem segments of the river between the juncture with the Ocklawaha River and the river 

mouth at Mayport, with the marine portion occurring between Julington Creek and the 

mouth. A SSAC was developed for DO in the marine portion of the river. It was 

approved by EPA in 2006 and is in effect as a WQS. The TMDL contains TN and TP 

protective loads in the freshwater portion of the LSJR and a TN protective load in the 

saline portion of the LSJR. These loads are set at a level necessary to achieve the marine 

DO SSAC and protect the statewide standard for DO in the freshwater section. The 

TMDL also contains a water quality target for chlorophyll a that is intended to implement 

the State’s narrative nutrient criterion. 

Similar to the modeling approach proposed by EPA for Florida estuaries, TN, TP, 

and chlorophyll a criteria were derived for the LSJR using linked watershed, 

hydrodynamic, and water quality models. Non-point nutrient inputs from the watershed 

to the river were determined for each sub-basin in the LSJR using the Pollutant Load 

Screening Model (PLSM), estimates of atmospheric deposition, and estimates of loading 

from tributaries and upstream. Within the river, hydrodynamics were modeled using the 

Environmental Fluid Dynamics Code (EFDC) model and water quality processes were 
Page 112 of 221

modeled using the U.S. Army Corps of Engineers Quality Integrated Compartment 

Model (CE-QUAL-ICM), Version 2. The models were calibrated for the period from 

January 1, 1995 to November 30, 1998. TMDL model scenarios were assessed on an 

annual basis to determine if chlorophyll a levels exceeded the chlorophyll a threshold of 

40 μg/L less than 10% of the time that was set as the water quality target to prevent 

undesirable shifts in algal community composition.

For Mosquito Lagoon, a suite of five approaches are considered to develop a 

weight of evidence by which numeric nutrient criteria can be developed. These 

approaches are based upon one of three relationships: 1) the link between nutrients, 

phytoplankton growth (as shown by chlorophyll a), and the trophic state of a system; 2) 

the link between nutrients, phytoplankton growth (as shown by chlorophyll a), the effects 

of phytoplankton on light attenuation in the water column, and the light requirements of 

seagrasses; or 3) the connection between TP and harmful algal bloom (HAB) occurrence. 

The first and primary approach uses a reference period from 2004-2008 to calculate 

annual median and maximum wet season medians of chlorophyll a, TN, and TP. The 

reference time period was selected because the TN, TP, and chlorophyll a observed 

during that period were low, the rainfall amounts during that period were representative 

of typical rainfall over time, and the Trophic State Index value for that time period was 

greater than 50, which is considered to be "good" (mesotrophy to oligo-mesotrophy). 

The second approach draws upon an optical model linking chlorophyll a to 

previously established light attenuation targets as a way to predict annual median 

chlorophyll a in southern Mosquito Lagoon that would be protective of seagrass and 

serve as a basis for criteria derivation. A third approach derives a TP level that 
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corresponds to minimum "bloom" levels of the dinoflagellate Pyrodinium bahamense, the 

common HAB species seen primarily in the southern Lagoon. A fourth line of evidence 

applied to the Mosquito Lagoon is multivariate geometric mean function regression 

models relating TN and TP to chlorophyll a on an annual basis and during the wet 

season. The final method is based on two general nutrient models.

201 Targets for 

chlorophyll a are set based on the reference period mentioned earlier for the north and 

central segments and the optical model for the southern segments. The reference method 

is used to derive the TN, TP, and chlorophyll a criteria for the Mosquito Lagoon with the 

other four methods providing supporting evidence. Two criteria magnitudes for TN, TP, 

and chlorophyll a are presented; one an annual median value and the other a wet season 

(July-September) median value. 

The approaches used for the Indian River Lagoon (IRL) and Banana River 

Lagoon (BRL) are similar to those used for Mosquito Lagoon. The approaches are based 

upon a weight of evidence relying on two general ecological relationships: 1) the link 

between nutrients, phytoplankton growth (as shown by chlorophyll a), and the trophic 

state of a system; and 2) the link between nutrients, phytoplankton growth (as shown by 

chlorophyll a), the effects of phytoplankton on light attenuation in the water column, the 

light requirements of seagrasses, and the previously established depth limit for 

seagrasses. The influence of TP on HAB events is also discussed as an ancillary line of 

evidence. As a first line of evidence loading limits are derived based on analyses done for 

TMDLs in 2009. The loading limits were established using regression models that regress 

 201 Steward, J.S., and E.F. Lowe. 2010. General empirical models for estimating nutrient load limits for 

Florida’s estuaries and inland waters. Limnology and Oceanography 55(1):433-445.

Dettmann, E.H. 2001. Effect of water residence time on annual export and denitrification of nitrogen in 

estuaries: A model analysis. Estuaries 24(4):481-490.
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seagrass depth limit targets against loading of TN and TP.202 The second method used 

annual medians of data from reference segments that meet desired depth thresholds 

established by the TMDL analyses. The third approach relies upon an optical model 

similar to the one described earlier for the Mosquito Lagoon using data from 1996-2007. 

A model was built for each of the sub-lagoons: the BRL, North IRL, and Central IRL 

(divided into Sebastian and South Central reaches). An optical model is in development 

for the North Central reach. The fourth approach also applies two general models to data 

specific to the IRL and BRL.203 Where the Dettmann (2001) model could not be used to 

predict TN concentrations, a TN:TP ratio for the given sublagoon was applied to the TP 

limit to calculate TN limits. The fifth approach relies upon the relationship between HAB 

occurrence and TP concentrations. Targets for chlorophyll a are presented as a range of 

values established using the optical model approach and the reference segment approach. 

Proposed TN and TP loading criteria are based on the loading limits established using the 

TMDL analyses. Primary proposed TN and TP criteria concentrations are calculated 

based on the reference segment method. Alternate criteria are proposed using a 

convergence of the concentrations calculated by the reference segment method and 

general models. Two criteria magnitudes are proposed, one for an annual median and the 

other for a wet season (June-October) monthly maximum.

The SJRWMD proposed criteria for the Tolomato and Matanzas Estuary (TME) 

using a weight of evidence approach and methods similar to those used in the other 

 202 Steward J.S., R.V. Virnstein, L.J. Morris, and E.F. Lowe. 2005. Setting Seagrass Depth, Coverage, and 

Light targets for the Indian River Lagoon system, Florida. Estuaries 6:923-935. 203 Steward, J.S., and E.F. Lowe. 2010. General empirical models for estimating nutrient load limits for 

Florida’s estuaries and inland waters. Limnology and Oceanography 55(1):433-445.

Dettmann, E. H. 2001. Effect of water residence time on annual export and denitrification of nitrogen in 

estuaries: A model analysis. Estuaries 24:481-490.
Page 115 of 221

estuaries. TN and TP concentrations and chlorophyll a target concentrations are based on 

an approach that analyzes water quality and estimated current loading during a reference 

period from 2000-2009. The period of reference was selected based on a desirable TSI 

score (<50), rainfall amounts typical of average conditions, and completeness of the data 

record. Criteria magnitudes are proposed as an annual median or mean and a maximum 

wet season (June-September) median or mean. The reference period approach of criteria 

derivation for the TME is supported by an additional line of evidence using regression 

analyses of chlorophyll a versus TN and TP. Target chlorophyll a values are based on the 

reference period analyses. The general nutrient models of Steward and Lowe (2010) and 

Dettmann (2001) are also used as an additional method by which to estimate loading 

limits and concentrations associated with those limits.

The SJRWMD also derived proposed criteria for the Halifax River Estuary. 

SJRWMD derived criteria using three methods. The first is a reference condition based 

on the period from 2000-2008. This period is selected because of the low TN levels 

compared to the previous decade, the low chlorophyll a concentrations which are 

consistent with chlorophyll a targets established for other estuaries throughout the State, 

and the "good" trophic status shown by TSI values less than 50. Concentrations are 

calculated using annual median concentrations and maximum wet-season median 

concentrations (as the highest monthly values from July-September) of TN, TP, and 

chlorophyll a. Simple linear regressions are used as a second line of evidence to calculate 

TN and TP criteria based on chlorophyll a targets established by the reference period 

calculations. The general nutrient models of Steward and Lowe (2010) and Dettmann 

(2001) are used as a final method by which to estimate loading limits and concentrations 
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associated with those limits. Proposed loading and concentration criteria for the North 

Halifax River Estuary are based on the loading and concentration estimates of the general 

nutrient models, with estimates of loadings from wastewater treatment facilities in the 

estuary removed to represent reference conditions. The current estimated concentrations 

(ca. 2004) of TN and TP based on the reference approach are proposed as criteria for the 

South Halifax River Estuary. Target chlorophyll a values for both segments are 

calculated using the reference period approach.

EPA is also considering the use of approaches outlined in Steward et al. (2005) to 

derive criteria in Indian River Lagoon. In particular EPA is considering using the depth 

of colonization within reference segments as “upper restoration depths” and the highest 

value observed for a specific segment as a minimum target for that segment. For more 

information regarding the derivation of these criteria, please see the TSD (Volume 1: 

Estuaries, Sections 2.18.9 (Indian River Lagoon), 2.19.9 (Halifax River), 2.20.9 (GTMP), 

and 2.21.9 (St Johns River)). 

3) Request for Comment on Proposed and Alternative Approaches

EPA believes that the proposed approach for each estuarine system is appropriate, 

scientifically defensible, and results in numeric nutrient criteria that protect the State’s 

designated uses to ensure that nutrient concentrations of a body of water support balanced

natural populations of aquatic flora and fauna. EPA requests comment on this systemspecific approach and the resulting numeric nutrient criteria. EPA also solicits additional 

available scientific information that can be used to derive numeric nutrient criteria to 

provide protection of fish consumption, recreation, and the propagation and maintenance 
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of a healthy, well-balanced population of fish and wildlife and protect Florida’s Class II 

and III estuarine waters from nitrogen and phosphorus pollution. 

In addition, EPA requests comment on the alternative approaches developed by 

the St. Johns River Water Management District for waters under their jurisdiction. 

Specifically, EPA requests comment on the scientific defensibility of these approaches,

as well as whether application of these approaches will result in numeric nutrient criteria

that will protect Class II and III estuarine waters in the State of Florida. EPA also 

requests comment on promulgating the alternative criteria in lieu of EPA’s proposed 

criteria.

b) Proposed Criteria Duration and Frequency (Estuaries)

Aquatic life water quality criteria include magnitude, duration, and frequency 

components. For EPA’s proposed TN, TP, and chlorophyll a criteria for estuarine waters, 

the criterion-magnitude values (expressed as concentrations) are provided in Table III.B1, the criterion-duration (or averaging period) is specified as annual, and the criterionfrequency is specified as a no-more-than-once-in–three-years excursion frequency of the 

annual geometric mean. EPA is proposing a criteria-duration of one year, in which 

sampled nutrient concentrations are summarized as annual geometric means to be 

consistent with the data set used to derive these criteria, which relied on either annual 

average nutrient concentrations or annual nutrient loading to the water body. EPA’s 

proposed excursion frequency of no-more-than-once-every-three-years is intended to 

minimize negative effects on designated uses as it will allow water bodies enough time to 

recover from occasionally elevated levels of nitrogen and phosphorus concentrations.204

 204 Boynton, W.R., J.D. Hagy, L. Murray, C. Stokes, and W.M. Kemp. 1996. A comparative analysis of 
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These duration and frequency components of the criteria are identical to those finalized in 

EPA’s rule for Florida’s lakes and flowing waters (40 CFR section 131.43), which will 

add consistency to the implementation of these criteria with those established in the 

previous rulemaking for upstream waters. Finally, the 3-year evaluation period provides a 

sufficient representation of average water body characteristics in the majority of cases, 

because it balances both short-term and long-term variation, while not imposing undue 

monitoring expectations. EPA requests comment on the frequency and duration 

components of these criteria and whether the three components of the criteria (magnitude, 

duration, and frequency) taken in combination will ensure protection of the designated 

uses of these waters. 

c) Proposed DPVs (Estuaries)

EPA is proposing a procedure to establish numeric TN and TP criteria for streams 

in Florida to protect the downstream estuarine water bodies that ultimately receive 

nitrogen and phosphorus pollution from these streams. These numeric nutrient criteria, 

which EPA refers to as Downstream Protection Values, or DPVs, would apply at each 

stream’s point of entry into the downstream water, referred to as the pour point. 

However, as explained more fully in Section I.A, EPA does not intend to finalize these 

DPVs if the district court modifies the Consent Decree consistent with EPA’s amended 

determination that numeric DPVs are not necessary to meet CWA requirements in 

Florida. EPA selected the pour point as the location to apply DPVs because the 

downstream waters respond to the nutrient inputs from the pour point, and all 

contributions from the network of flowing waters above this point affect the water quality 

 

eutrophication patterns in a temperate coastal lagoon. Estuaries 19(2B):408-421.
Page 119 of 221

at the pour point. If the DPV is not attained at the point of entry into the estuary, then the 

collective set of streams in the upstream watershed does not attain the DPV, for purposes 

of CWA section 303(d). 

The Agency is proposing a hierarchical procedure that includes four approaches 

for setting TN and TP DPVs. EPA’s intention in proposing the four approaches is to 

provide a range of methods for the State to derive TN and TP DPVs that reflect the data 

and scientific information available. Water quality modeling is the most rigorous and 

most data-demanding method, and will generally result in the most refined DPVs. Water 

quality modeling is EPA’s preferred method for establishing DPVs and is listed first in 

the hierarchy. It is followed by less rigorous methods that are also less data-demanding. 

Using a procedure from a lower tier of the hierarchy requires less data, but also generally 

results in more stringent DPVs to account for the uncertainties associated with these less 

refined procedures. The methods available to derive DPVs should be considered in the 

following order:

1. Water quality simulation models to derive TN and TP values,

2. Reference condition approach based on TN and TP concentrations at

the stream pour point, coincident in time with the data record from

which the downstream receiving estuary segment TN and TP criteria 

were developed using the same data quality screens and reference 

condition approach, 

3. Dilution models based on the relationship between salinity and 

nutrient concentration in the receiving segment, and
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4. The TN and TP criteria from the receiving estuary segment to which 

the freshwater stream discharges, in cases where data are too limited to 

apply the first three approaches.

All four approaches are briefly described in the following discussion. A more 

detailed description of the approaches, as well as the TN and TP DPVs that result from

using each of the approaches, is provided in the technical support document (Volume 1: 

Estuaries, Section 1.6).

EPA believes that the first approach, the use of water quality simulation models, 

is the most refined method to define a DPV at the stream’s pour point that will support 

balanced natural populations of aquatic flora and fauna in the downstream estuary. This 

approach may be appropriate when water quality simulation models are available, such as 

in the estuarine systems where mechanistic models were used to derive criteria. The 

modeled nutrient loads entering the estuaries that result in attainment of the biological 

endpoints within the estuaries can be used to derive DPVs by computing the annual 

geometric mean TN and TP concentrations that correspond with the modeled loads at the 

pour point of each stream for each of the years 2002 through 2009. Because EPA used 

coupled watershed and estuarine models to establish the estuary criteria (in some 

locations), EPA is confident that the watershed modeling provides concentrations that are 

protective of corresponding estuarine biological endpoints. Therefore EPA selected the 

90th percentile from the distribution of annual geometric means of modeled loads as the 

DPV to be consistent with the use of the 90th percentile used to derive the criteria 

protective of the estuary using the mechanistic models (Volume 1: Estuaries, Section 

1.6).
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EPA is proposing the second DPV approach, a reference condition approach, for 

estuarine systems where water quality simulation models are not available, and where a

reference condition approach is used to derive estuary TN, TP, and chlorophyll a criteria. 

Since the downstream estuary is supporting balanced natural populations of aquatic flora 

and fauna during the reference condition period, the nutrient loads passing through the 

pour points into the estuary during that same period should be protective of the estuary. 

Therefore, EPA believes it would be appropriate in these cases to derive reference

condition-based DPVs using water quality data at the pour point of the freshwater 

streams, coincident in time with the data record from which EPA derived the downstream 

estuary segment TN and TP criteria. EPA proposes that the same data screens and 

reference condition approach be applied to the pour point data as were applied to the 

estuary data when deriving DPVs using this approach. This will prevent deriving a DPV 

using upstream water quality data that coincided with a documented downstream impact

(e.g., CWA section 303(d) listing for nutrients in the estuary segment) and ensure 

mathematical consistency between the DPVs and estuarine criteria. 

EPA is proposing the third DPV approach for estuarine systems where water 

quality simulation models are not available. For example, this approach may be 

appropriate in the Indian River Lagoon, the Halifax River, and the GTMP estuarine 

systems where EPA used statistical models to derive the criteria protective of the estuary. 

In these areas, EPA believes it would be appropriate to derive DPVs using dilution 

models based on the relationship between salinity and nutrient concentration. The 

concept is that the tidal mixing or dilution can be estimated from the estuarine salinity. 

By plotting observed estuarine TN or TP versus the estuarine salinity and fitting a linear 
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regression, the TN or TP at various levels of salinity can be determined. This regression 

model can then be used to determine the TN or TP concentration at the pour point that 

will ensure attainment and maintenance of the estuarine numeric nutrient criteria 

concentration. The TN and TP DPV for the inflowing canal or stream can be determined 

from the point on the regression line having the same salinity as the pour point, which is 

by definition 2.7 psu.

EPA’s fourth proposed approach for establishing DPVs is to apply the 

downstream receiving estuary segment TN and TP criteria as shown in Table III.B-1 to 

the pour point as the DPVs. This is the simplest approach and may be appropriate where 

data are too limited to apply the first three approaches. As noted in Table III.B-1, Florida 

derived numeric nutrient criteria for Clearwater Harbor, Tampa Bay, Sarasota Bay, and 

Charlotte Harbor estuaries that can be found in Section 62-302.532(a)-(d), F.A.C. 

Therefore, the applicable DPVs for those four estuaries would be Florida’s estuary 

criteria in Section 62-302.532(a)-(d), F.A.C. if using this fourth proposed approach for 

establishing DPVs. 

EPA believes the proposed approaches for deriving DPVs establish a decisionmaking framework that is binding, clear, predictable, and transparent. Therefore, EPA is 

proposing that DPVs derived using these approaches do not require EPA approval under 

Clean Water Act section 303(c) to take effect.205 A DPV calculated under options 2, 3, 

and 4 may be more stringent than a DPV calculated using a water quality model. These 

alternative options are intended to ensure that water quality standards are not only 

restored when found to be impaired, but are maintained when found to be attained, 

 205 65 FR 24641, 24648 (April 27, 2000).
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consistent with the CWA. Higher levels of TN and/or TP may be allowed in watersheds 

where it is demonstrated that such higher levels will fully protect the estuary’s WQS. To 

the extent that it is determined that the alternative option DPVs for a given estuary are 

over-protective, applying a water quality model as set out in EPA’s option 1 would result 

in a more refined definition of the DPV for that estuary.

EPA believes that these proposed approaches to establish DPVs are appropriate, 

scientifically defensible, and result in numeric values that will ensure the attainment and 

maintenance of the downstream estuarine criteria. EPA requests comment on these 

approaches. EPA also requests comment on the alternative approach of finalizing the 

numeric TN and TP DPVs that EPA calculated using these approaches (as provided in 

Volume 1: Estuaries, Section 1.6 of the technical support document) in place of the 

proposed approaches. Finally, EPA solicits additional available scientific information that 

can be used to ensure attainment and maintenance of the downstream estuarine criteria. 

Commenters who submitted comments or scientific information related to DPVs for 

estuaries during the public comment period for EPA’s proposed inland waters rule (75 

FR 4173) should reconsider their previous comments in light of the new information 

presented in this proposal and must re-submit their comments during the public comment 

period for this rulemaking to receive EPA response. 

d) Proposed Approach and Criteria for Tidal Creeks

Tidal creeks are relatively small coastal tributaries that lie at the transition zone 

between terrestrial uplands and the open estuary. They are small sub-estuaries that exhibit 

a wide range of salinities typical of larger estuaries, but on a smaller scale. Tidal creeks

are important spawning and nursery areas for aquatic life in adjacent estuary and coastal 
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systems. They typically receive freshwater flow from streams and groundwater, similar to 

estuaries, but have less developed drainage systems. Alternatively, some tidal creeks are

dominated by mangroves and other wetland vegetation with no freshwater stream inputs, 

and serve as conduits for tidal water to enter and leave wetland areas. Water quality and 

biological conditions are different in tidal creeks compared to estuarine systems due to 

relatively small drainage areas, narrow stream channels, shallow depths, and the 

influence of adjacent marsh and mangrove habitats. 

EPA reviewed the available scientific information and has determined that there 

are insufficient data and research at this time to develop separate numeric nutrient criteria 

specifically for tidal creeks. EPA, therefore, proposes to apply the TN and TP criteria 

developed for either the adjacent freshwater or estuarine segments to each tidal creek in 

Florida, depending on the tidal creek’s salinity levels. If the mean chloride concentration 

of the tidal creek is < 1,500 mg/L, EPA proposes to apply the TN and TP criteria from the

adjacent freshwater segment (as defined in 40 CFR 131.43).

206 If the mean chloride 

concentration of the tidal creek is > 1,500 mg/L, EPA proposes to apply the chlorophyll 

a, TN, and TP criteria from the adjacent estuary segment (as defined in Section III.B of 

this proposed rulemaking). Alternatively, EPA requests comment on applying the more 

stringent of the two sets of criteria, freshwater or estuarine, to tidal creeks with varying 

salinity levels. For more information please see the TSD (Volume 1: Estuaries, Section

3.1).

 206 EPA did not establish chlorophyll a criteria for freshwater streams due to lack of available approaches to 

interpret existing data to infer scientifically supported thresholds for these nutrient-specific response 

variables in Florida streams.
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As a second alternative option, EPA could use the mean salinities for each tidal 

creek to interpolate TN and TP concentrations between freshwater and estuarine criteria 

from adjacent freshwater and estuarine segments. TN and TP vary predictably along a 

salinity gradient, allowing for this interpolation where salinity data are available. The 

calculation EPA could use for this interpolation is provided in the TSD (Volume 1: 

Estuaries, Section 3.1). 

EPA believes that the proposed approach for tidal creeks is appropriate, 

scientifically defensible, and results in numeric nutrient criteria that protect the State’s 

designated uses and ensure that nutrient concentrations of a body of water support 

balanced natural populations of aquatic flora and fauna. EPA requests comment on the 

proposed option and the alternative. EPA also requests additional available scientific 

information that can be used to provide protection for fish consumption, recreation, and 

the propagation and maintenance of a healthy, well-balanced population of fish and 

wildlife to protect Florida’s tidal creeks from nitrogen and phosphorus pollution. 

e) Proposed Approach and Criteria for Marine Lakes

Marine lakes are coastal lakes and ponds with groundwater or intermittent surface 

water connections to marine water. They do not have a permanent surface connection to 

tidal waters. They are small and shallow, and generally round or elliptical in shape, as 

they were formed from depressions that became isolated from marine waters by sand and 

dune formation. Some marine lakes are stratified by a salinity gradient where a 

freshwater layer at the surface is separated from a denser saline layer below. Similar to 

inland lakes, marine lakes in Florida are generally oligotrophic under undisturbed 

conditions with low nitrogen and phosphorus concentrations and low productivity. Their 
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oligotrophic nature and stratification make them susceptible to the adverse effects of 

nitrogen and phosphorus pollution. EPA analyzed the data from over 50 marine lakes in 

Florida and found that chlorophyll a responded to TN and TP in a similar fashion, based 

on color and alkalinity, as freshwater inland lakes. Details and supporting documentation 

are provided in the TSD (Volume 1: Estuaries, Section 3.2). 

EPA is proposing to apply the criteria developed for freshwater inland lakes in 

EPA’s December 6, 2010 rulemaking for Florida’s lakes and flowing waters (40 CFR 

131.43) to protect the designated uses in marine lakes since marine lakes have a similar

trophic condition expectation and chlorophyll a response to nutrient concentrations. The 

criteria EPA proposes to apply to marine lakes are those found in 40 CFR 131.43 and 

replicated in Table III.B-2.

Table III.B-2. EPA’s Proposed Numeric Criteria for Florida’s Marine Lakes

Long Term Average Lake 

Color

a and Alkalinity

EPA Final 

Chl-ab,*

μg/L

EPA Final TN and TP Criteria

[Range]

TN

mg/L

TP

mg/L

Colored lakesc 20 1.27

[1.27-2.23]

0.05

[0.05-0.16]

Clear lakes, high 

alkalinityd

20 1.05

[1.05-1.91]

0.03

[0.03-0.09]

Clear lakes, low 

alkalinitye

6 0.51

[0.51-0.93]

0.01

[0.01-0.03] a Platinum-cobalt units (PCU) assessed as true color free from turbidity b Chl-a is defined as corrected chlorophyll, or the concentration of chl-a remaining

after the chlorophyll degradation product, phaeophytin a, has been subtracted from the uncorrected

chl-a measurement. c Long-term color > 40 PCU and alkalinity > 20 mg/L CaCO3 d Long-term color ≤ 40 PCU and alkalinity > 20 mg/L CaCO3 e Long-term color ≤ 40 PCU and alkalinity ≤ 20 mg/L CaCO3

* For a water body, the annual geometric mean of chl-a, TN or TP concentrations shall

not exceed the applicable criterion concentration more than once in a three-year period.
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EPA believes that the proposed approach for marine lakes is appropriate, 

scientifically defensible, and results in numeric nutrient criteria that protect the State’s 

designated uses and ensure that nutrient concentrations of a body of water support 

balanced natural populations of aquatic flora and fauna. EPA requests comment on the 

proposed approach. EPA also solicits additional available scientific information that can 

be used to provide protection for fish consumption, recreation, and the propagation and 

maintenance of a healthy, well-balanced population of fish and wildlife to protect 

Florida’s marine lakes from nitrogen and phosphorus pollution.

C. Proposed Numeric Criteria for Coastal Waters

1. Introduction 

EPA is defining coastal waters in this proposed rulemaking as marine waters that 

start at the land margin and extend up to three nautical miles from shore, with chloride 

concentrations greater than 1,500 mg/L, excluding estuaries. Unlike estuaries, which are 

typically highly influenced by freshwater flows and can be organized within boundaries, 

coastal waters are less confined, with open connections to ocean waters, and have 

localized influences from freshwater sources near the estuary/coastal boundary (i.e., 

estuary pass). 

EPA is proposing to derive chlorophyll a criteria for coastal waters using satellite 

remote sensing, where possible. This approach is possible for all coastal waters except 

those in the Big Bend Coastal region. In the Big Bend Coastal region (waters offshore of 

Apalachicola Bay, Alligator Harbor, Ochlockonee Bay, Big Bend/Apalachee Bay, 

Suwannee River, and Springs Coast), seagrass beds and CDOM export from rivers 
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confound interpretation of satellite data and derivation of chlRS-a. EPA’s proposed 

approach and criteria for the Big Bend Coastal region is discussed in Section III.B. 

2. Proposed Numeric Criteria (Coastal Waters)

EPA is proposing numeric chlorophyll a criteria, as measured by remotely sensed 

numeric chlorophyll a (chlRS-a), for 71 segments in three coastal regions of Florida 

classified as Class III waters under Florida law (Section 62-302.400, F.A.C.). A map 

showing the locations of the coastal segments can be found in the TSD (Volume 2: 

Coastal Waters, Section 1.3). EPA’s proposed coastal criteria are listed in Table III.C-1.

Table III.C-1. EPA’s Proposed Numeric Criteria for Florida’s Coastal Waters

Coastal Region Coastal Segment+ Approximate Location ChlorophyllRS-a1

* (mg/m3)

Panhandle

1 Alabama border 2.41

2 Pensacola Bay Pass 2.57

3 1.44

4 1.16

5 1.06

6 1.04

7 1.14

8 Choctawhatchee Bay Pass 1.23

9 1.08

10 1.09

11 1.11

12 1.18

13 1.45

14 St. Andrews Bay Pass 1.74

15 St. Joseph Bay Pass 2.75

16 2.39

17 Southeast St. Joseph Bay 3.47

West Florida 

Shelf

18 3.96

19 Tampa Bay Pass 4.45

20 3.37

21 3.25

22 2.95

23 2.79

24 2.98

25 3.24

26 Charlotte Harbor 4.55
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27 4.22

28 3.67

29 4.16

30 5.70

31 4.54

32 4.03

33 Fort Myers 4.61

Atlantic Coast

34 Biscayne Bay 0.92

35 0.26

36 0.26

37 0.24

38 0.21

39 0.21

40 0.20

41 0.20

42 0.21

43 0.25

44 0.57

45 St. Lucie Inlet 1.08

46 1.42

47 1.77

48 1.55

49 1.44

50 1.53

51 1.31

52 1.40

53 1.80

54 Canaveral Bight 2.73

55 2.33

56 2.28

57 2.06

58 1.92

59 1.76

60 1.72

61 2.04

62 1.92

63 1.86

64 1.95

65 2.41

66 2.76

67 2.80

68 3.45

69 Nassau Sound 3.69

70 3.78

71 Georgia border 4.22 1 ChlorophyllRS-a is remotely sensed calculation of chlorophyll a concentrations. 

* For a given water body, the annual geometric mean of the chlorophyll a concentration shall not exceed 

the applicable criterion concentration more than once in a three-year period. + Please see TSD for location of Coastal Segments (Volume 2: Coastal Waters, Section 1.3).
Page 130 of 221

As discussed in Section III.A.1.b, EPA is not proposing TN and TP criteria for 

Florida’s coastal waters.

a) Summary of Approaches

1) Proposed Approach (Coastal Waters)

EPA conducted a comprehensive review of water body-specific water quality and 

impairment information as detailed in Section III.A.3.a. EPA determined through this 

review that at most times, Florida coastal waters appear to be supporting balanced natural 

populations of aquatic flora and fauna. EPA removed data from criteria computations in 

the limited instances where the Agency found that coastal waters were listed on the 

State’s CWA section 303(d) list to ensure the resulting dataset was representative of 

times and locations that these waters were supporting balanced natural populations of 

aquatic flora and fauna. Therefore, EPA is proposing to use a reference condition 

approach using data collected from satellite remote sensing of chlorophyll a. 

To derive proposed criteria for coastal areas, EPA chose to use chlRS-a

measurements from the SeaWiFS satellite because it had the longest and earliest 

historical record.

207 From the satellite measurements, screened to reflect conditions 

supportive of balanced natural populations of flora and fauna, EPA calculated criteria as 

the 90th percentile of the annual geometric means of chlRS-a values over the 1998-2009 

period in each coastal segment (For a discussion of EPA’s selection of the 90th percentile

to derive the proposed coastal criteria, see Section III.A.3.a and the TSD (Volume 2: 

Coastal Waters)). 

 207 NOTE: SeaWiFS was replaced by MODIS and MERIS satellite generated data. EPA has developed an 

approach that can utilize any new satellite data sources for ongoing assessment purposes.
Page 131 of 221

b) Request for Comment on Proposed Approach

EPA believes that the proposed approach for coastal waters is appropriate, 

scientifically defensible, and results in numeric nutrient criteria that protect the State’s 

designated uses and ensure that nutrient concentrations of a body of water support 

balanced natural populations of aquatic flora and fauna. EPA requests comment on this 

approach and the resulting numeric nutrient criteria. EPA also solicits additional available 

scientific information that can be used to provide protection of fish consumption, 

recreation and the propagation and maintenance of a healthy, well-balanced population of 

fish and wildlife and protect Florida’s Class III coastal waters from nitrogen and 

phosphorus pollution. 

c) Proposed Criteria Duration and Frequency (Coastal Waters)

For EPA’s proposed chlorophyll a criteria for coastal waters, the criterionmagnitude values (expressed as concentrations) are provided in Table III.C-1, the 

criterion-duration (or averaging period) is specified as annual, and the criterion-frequency 

is specified as no-more-than-once-every-three-years. EPA is proposing a criteria-duration 

of one year, in which sampled chlorophyll a concentrations are summarized as annual 

geometric means, to be consistent with the data set used to derive these criteria, which 

relied on annual average concentrations. EPA’s proposed excursion frequency of nomore-than-once-every-three-years is intended to minimize negative effects on designated 

uses as it will allow water bodies enough time to recover from occasionally elevated 

chlorophyll a concentrations.

208 These duration and frequency components of the criteria 

 208 Boynton, W.R., J.D. Hagy, L. Murray, C. Stokes, and W.M. Kemp. 1996. A comparative analysis of 
Page 132 of 221

are identical to those finalized in EPA’s rule for Florida’s lakes and flowing waters (40 

CFR 131.43), which will add consistency to the implementation of these criteria with 

those established in the previous rulemaking. Finally, the 3-year evaluation period 

provides a sufficient representation of average water body characteristics in the majority 

of cases, because it balances both short-term and long-term variation, while not imposing 

undue monitoring expectations. EPA requests comment on the frequency and duration 

components of these criteria and whether the three components of the criteria (magnitude, 

duration and frequency) taken in combination will ensure protection of the designated 

uses of these waters. 

D. Proposed Numeric Criteria for South Florida Inland Flowing Waters

1. Proposed Numeric Criteria (South Florida Inland Flowing Waters) 

For purposes of this proposal, EPA is defining “south Florida inland flowing 

waters” as inland predominantly fresh surface waters that have been classified as Class I 

or Class III in the South Florida Nutrient Watershed Region, which encompasses the 

waters south of Lake Okeechobee, the Caloosahatchee River (including Estero Bay) 

watershed, and the St. Lucie watershed. This area contains more than 1,700 miles (2,736 

km) of canals, dikes, and levees that control the movement of freshwater in south Florida. 

Some of the significant land management units within south Florida include the 

Everglades Agricultural Area, the Loxahatchee National Wildlife Refuge (Water 

Conservation Area 1), Water Conservation Areas 2 and 3, Big Cypress National Preserve, 

Everglades National Park, Biscayne Bay National Park, and the Florida Keys National 

 

eutrophication patterns in a temperate coastal lagoon. Estuaries 19(2B):408- 421.
Page 133 of 221

Marine Sanctuary. A map showing this region is provided in the TSD (Volume 3: South 

Florida Inland Flowing Waters, Section 3).

EPA is proposing that TN and TP DPVs be derived using the approaches outlined 

in Section III.D.2 for 22 pour points in south Florida, outside of the Everglades 

Protection Area (EvPA) and Everglades Agricultural Area (EAA), where inland flowing 

waters discharge into south Florida marine waters (Biscayne Bay, Florida Bay, and 

marine waters on the southeast and southwest coasts). For south Florida, EPA is 

proposing the use of DPVs to manage nitrogen and phosphorus pollution in the inland 

flowing waters and protect the water quality of estuaries and coastal waters downstream. 

Therefore, the applicable numeric nutrient criteria for south Florida inland flowing 

waters, outside the lands of the Miccosukee and Seminole Tribes, EvPA, and the EAA, 

would consist solely of the south Florida marine water DPVs. The calculated DPVs using 

the approaches in Section III.D.2 for the 22 pour points are presented in the TSD

(Volume 3: South Florida Inland Flowing Waters, Section 2).

The proposed approaches to derive DPVs that EPA is proposing for south Florida 

inland flowing waters do not apply to flowing waters (canals) within the EvPA or the 

EAA. There is an existing TP criterion of 0.010 mg/L (10 ppb) that currently applies to 

the marshes and adjacent canals within the EvPA (Section 61-302.540, F.A.C.). EPA 

approved that TP criterion in 2005 as protective of the waters in the EvPA. EPA’s 

approval was upheld by the U.S. District Court in Miccosukee Tribe of Indians of 

Florida, et al. v. U.S. EPA.

209 For this proposal, EPA has determined that the existing TP 

criterion continues to be protective of the designated uses of the flowing waters in the 

 209 Miccosukee Tribe of Indians of Fla., et al. v. U.S. EPA, No. 1:04-cv-21448 ASG, 2008 WL 2967654 

(S.D. Fla. July 29, 2008). 
Page 134 of 221

EvPA and that no additional numeric nutrient criteria are necessary at this time for the 

EvPA. While the existing TP criterion does not apply directly to the flowing waters of the 

EAA, EPA has also determined that the TP criterion will serve to be protective of the 

designated uses of the flowing waters in the EAA. Most of the water flowing from the 

EAA currently passes through stormwater treatment areas (STAs) that have been 

specifically constructed to remove phosphorus from the water before it enters the EvPA. 

The waters discharging from the STAs are subject to CWA discharge permits that must 

include limits as stringent as necessary to meet the 10 ppb TP criterion in the EvPA. 

Efforts to reduce phosphorus upstream of the STAs (i.e., in the EAA) are currently 

underway to ensure the water discharged from the STAs will meet the TP criterion in the 

EvPA. Based on the combination of the actions that will be necessary to ensure that 

waters from the EAA do not cause an impairment of the downstream waters in the EvPA, 

EPA has determined that the existing TP criterion is the only numeric nutrient criterion 

that is necessary to protect the flowing waters of the EAA as well as the EvPA. 

Development of water quality standards for the EvPA and restoration actions within the 

EAA to attain the TP criterion have been and remain subject to the oversight of two 

federal district courts. EPA believes its decision not to propose additional numeric 

nutrient criteria for these areas is appropriate given the ongoing restoration efforts in the 

Everglades. For further information about ongoing EPA and FDEP actions related to 

Everglades restoration see: (1) http://www.epa.gov/aboutepa/states/fl.html, and (2) 

http://depnewsroom.wordpress.com/hot-topics/everglades/.

2. Proposed DPVs (South Florida)
Page 135 of 221

EPA is proposing a procedure to establish numeric TN and TP criteria for south 

Florida inland flowing waters to protect the downstream marine waters that ultimately 

receive nitrogen and phosphorus pollution from upstream sources. However, as explained 

more fully in Section I.A, EPA does not intend to finalize these DPVs if the district court 

modifies the Consent Decree consistent with EPA’s amended determination that numeric 

DPVs are not necessary to meet CWA requirements in Florida. Like the DPVs that EPA 

is proposing to protect estuaries in Florida, EPA is proposing the DPVs for south Florida 

inland flowing waters that will apply at each stream or canal’s point of entry into the 

downstream south Florida marine water. If the DPV is not attained at the pour point into 

the applicable marine water segment, then the collective set of flowing waters, including 

canals, in the upstream watershed does not attain the DPV, for purposes of CWA section 

303(d). 

The Agency is proposing a hierarchical procedure that includes four approaches 

for setting TN and TP DPVs. These are the same approaches EPA is proposing for the 

State to derive DPVs for Florida estuaries to reflect the data and scientific information 

available. The methods available to derive DPVs should be considered in the following 

order:

1. Water quality simulation models to derive TN and TP values,

2. Reference condition approach based on TN and TP concentrations at

the stream pour point, coincident in time with the data record from

which the downstream receiving marine water segment TN and TP 

criteria were developed using the same data quality screens and 

reference condition approach,
Page 136 of 221

3. Dilution models based on the relationship between salinity and 

nutrient concentration in the receiving segment, and

4. The TN and TP criteria from the receiving marine water segment to 

which the freshwater stream discharges, in cases where data are too 

limited to apply the first three approaches.

EPA’s intention in proposing the four approaches is to provide a range of methods 

for deriving TN and TP DPVs that reflect the degree of data and scientific information 

available. Water quality modeling is the most rigorous and most data-demanding method, 

and will generally result in the most refined DPVs. Water quality modeling is EPA’s

preferred method for establishing DPVs and is listed first in the hierarchy. Due to the 

highly modified and managed canal systems in south Florida, EPA did not develop 

mechanistic models for the region, however, EPA is including the option for use if 

mechanistic models are developed for south Florida in the future. EPA’s lead approach 

for calculating DPVs in south Florida is the reference condition approach. This approach

is followed by less rigorous methods that are also less data-demanding. Using a 

procedure from a lower tier of the hierarchy requires less data, but also generally results 

in more stringent DPVs to account for the uncertainties associated with these less refined 

procedures. 

All four approaches are briefly described in the following discussion. A more 

detailed description of the approaches, as well as the TN and TP DPVs that result from

using the lead approach, the reference condition approach, is provided in the technical 

support document (Volume 3: South Florida Inland Flowing Waters, Section 2).
Page 137 of 221

EPA believes that the first approach, the use of water quality simulation models, 

is the most refined method to define a DPV at the stream’s pour point that will support 

balanced natural populations of aquatic flora and fauna in the downstream marine water. 

This approach may be appropriate when water quality simulation models are available, 

such as in the estuarine systems where mechanistic models were used to derive the 

criteria protective of the estuary. 

EPA is proposing the second DPV approach, the reference condition approach,

where a reference condition approach is used to derive TN, TP, and chlorophyll a criteria

in the downstream marine water, as the lead approach for calculating DPVs in south 

Florida. Florida derived numeric nutrient criteria for TN, TP, and chlorophyll a in south 

Florida marine waters using a “Maintain Healthy Conditions Approach,” which derives 

criteria reflective of ambient water quality conditions (Section 62-302.532, F.A.C.). This 

approach is akin to EPA’s reference condition approach, which is designed to develop 

numeric nutrient criteria that are protective of applicable designated uses by identifying 

numeric nutrient criteria concentrations occurring in least-disturbed waters that are 

supporting designated uses. Since the downstream marine water is supporting balanced 

natural populations of aquatic flora and fauna during the reference condition period, the 

nutrient loads passing through the pour points into the marine water during the same 

period should be protective of the marine water. Therefore, EPA believes it would be 

appropriate in these cases to derive reference condition-based DPVs using water quality 

data at the pour point of the freshwater streams, coincident in time with the data record 

from which the downstream marine water segment TN and TP criteria were derived. EPA 

proposes that water quality data used to calculate DPVs at each pour point be screened to 
Page 138 of 221

prevent the use of upstream water quality data that coincided with a documented 

downstream impact. This will prevent deriving a DPV using upstream water quality data 

that coincided with a documented downstream impact (e.g., CWA section 303(d) listing 

for nutrients in the marine water segment) and ensure mathematical consistency between 

the DPVs and marine water criteria. 

The third DPV approach is also available for south Florida marine systems where 

water quality simulation models are not available. In these areas, EPA believes it would 

be appropriate to derive DPVs using dilution models based on the relationship between 

salinity and nutrient concentration. The concept is that the tidal mixing or dilution can be 

estimated from the marine water salinity. By plotting observed marine water TN or TP 

versus the marine water salinity and fitting a linear regression, the TN or TP at various 

levels of salinity can be determined. This regression model can then be used to determine 

the TN or TP concentration at the pour point associated with the average marine water 

salinity that will ensure the attainment and maintenance of the marine water numeric 

nutrient criteria concentration.

EPA’s fourth approach for establishing DPVs is to apply the downstream 

receiving marine water segment TN and TP criteria to the pour point as the DPVs. This is 

the simplest approach and may be appropriate where data are too limited to apply the first 

three approaches. Florida derived numeric nutrient criteria for south Florida marine 

waters that can be found in Section 62-302.532(e)-(h), F.A.C. Therefore, the applicable 

DPVs for those south Florida marine waters would be Florida’s criteria in Section 62-

302.532(e)-(h), F.A.C. if using this fourth proposed approach for establishing DPVs. 
Page 139 of 221

EPA believes the proposed approaches for deriving DPVs establish a decisionmaking framework that is binding, clear, predictable, and transparent. Therefore, EPA is 

proposing that DPVs derived using these approaches do not require EPA approval under 

Clean Water Act section 303(c) to take effect.210 A DPV calculated under options 2, 3, 

and 4 may be more stringent than a DPV calculated using a water quality model. These 

alternative options are intended to ensure that water quality standards are not only 

restored when found to be impaired, but are maintained when found to be attained, 

consistent with the CWA. Higher levels of TN and/or TP may be allowed in watersheds 

where it is demonstrated that such higher levels will fully protect the marine water’s 

WQS. To the extent that it is determined that the alternative option DPVs for a given 

marine water are over-protective, applying a water quality model as set out in EPA’s 

option 1 would result in a more refined definition of the DPV for that marine water.

EPA believes that these proposed approaches to establish DPVs are appropriate, 

scientifically defensible, and result in numeric values that will ensure the attainment and 

maintenance of the downstream south Florida marine water criteria. EPA requests 

comment on these approaches. EPA also requests comment on the alternative approach of 

finalizing the numeric TN and TP DPVs that EPA calculated using these approaches (as 

provided in Volume 3: South Florida Inland Flowing Waters, Section 2 of the technical 

support document) in place of the proposed approaches. Finally, EPA solicits additional 

available scientific information that can be used to ensure attainment and maintenance of 

the downstream south Florida marine water criteria. Commenters who submitted 

comments or scientific information related to DPVs for estuaries during the public 

 210 65 FR 24641, 24647 (April 27, 2000).
Page 140 of 221

comment period for EPA’s proposed inland waters rule (75 FR 4173) should reconsider 

their previous comments in light of the new information presented in this proposal and 

must re-submit their comments during the public comment period for this rulemaking to 

receive EPA response.

a) Alternative Approach (South Florida Inland Flowing Waters)

As an alternative to EPA’s proposed DPV-only approach for south Florida inland 

flowing waters, EPA developed protective instream TN and TP criteria for Class I and III 

flowing waters (including canals and streams) in three inland subregions in south Florida 

(Biscayne, Palm Beach, and West) that are outside the lands of the Miccosukee and 

Seminole Tribes, EAA, and EvPA. EPA’s alternative criteria for south Florida inland 

flowing waters are listed in Table III.D-1.

Table III.D-1. EPA’s Alternative Numeric Criteria for South Florida’s Inland 

Flowing Waters

Subregion TN

(mg/L)

TP

(mg/L)

Biscayne 2 0.052

Palm Beach 2 0.052

West 2 0.052

EPA defined the boundaries of these three subregions based on patterns in 

geology/soils, hydrology, and vegetation. EPA compiled data for these subregions from 

IWR Run 40 and the South Florida Water Management District's DBHydro database. 

EPA screened the data to include freshwater locations and Class III waters, resulting in 

4,758 daily averages with matched chl-a, TN, and TP data. 
Page 141 of 221

Next, EPA chose to evaluate algal biomass, as indicated by chlorophyll a

concentrations, as a sensitive endpoint for numeric nutrient criteria development. Nutrient 

pollution can increase biomass of primary producers, especially algae, and have 

subsequent negative impacts on recreation and aquatic life. The application of algal 

biomass as an endpoint for criteria derivation in south Florida inland flowing waters, 

including canals, might be appropriate given the following observations: (1) flow in these 

water bodies is frequently reduced, leading to long residence times; (2) canopy cover is 

reduced both naturally and through manipulation, reducing light limitation; and (3) 

nutrient concentrations are elevated. Because both average chlorophyll a concentrations 

and instantaneous chlorophyll a concentrations (e.g. bloom conditions) can impact 

recreation and aquatic life, EPA chose to derive TN and TP criteria to reduce the

likelihood of increased nuisance algal blooms by relating maximum chlorophyll a to 

average annual chlorophyll concentrations. EPA defined nuisance algal bloom conditions 

as concentrations above 30 μg/L using trophic state boundaries, user perception studies, 

and observed impacts. EPA evaluated existing scientific literature on the frequency of 

occurrence of chlorophyll a levels, and selected a 10 percent occurrence of nuisance algal 

blooms as the maximum allowable frequency to prevent impairment of recreation and 

aquatic life in the three south Florida inland subregions.

211

EPA then used statistical models to derive TN and TP criteria to limit the 

frequency of occurrence of nuisance algal blooms in these waters, defined by chlorophyll 

a concentrations above 30 μg/L. The resulting TN and TP criteria represent the annual 

geometric mean of TN and TP concentrations from flowing waters in each of the three 

 211 Havens, K.E. and W.W. Walker. 2002. Development of a total phosphorus concentration goal in the 

TMDL process for Lake Okeechobee, Florida (USA). Lake and Reservoir Management 18(3):227-238.
Page 142 of 221

subregions that are associated with a 10 percent or lower frequency of nuisance algal 

bloom occurrence. If EPA were to finalize this alternative approach instead of EPA’s lead 

approach, these TN and TP criteria would apply throughout the flowing waters in each of 

the three subregions, not just at the pour points. If criteria are calculated using this 

alternative approach, DPVs for protecting downstream south Florida marine waters will 

still be calculated using the hierarchical approach in Section III.D.2, unless, as described 

more in Section I.A, the district court modifies the Consent Decree consistent with EPA’s 

amended determination that numeric DPVs are not necessary to meet CWA requirements 

in Florida. Additional details on this alternative approach are provided in the TSD 

(Volume 3: South Florida Inland Flowing Waters, Section 3). 

b) Request for Comment on Proposed and Alternative Approaches

EPA believes that the proposed approach for south Florida inland flowing waters 

is appropriate, scientifically defensible, and results in the protection of south Florida

inland flowing waters. EPA requests comment on this approach. EPA also solicits 

additional available scientific information that can be used to provide protection of fish 

consumption, recreation and the propagation and maintenance of a healthy, well-balanced 

population of fish and wildlife in south Florida’s Class I and III inland flowing waters

from nitrogen and phosphorus pollution. 

In addition, EPA requests comment on the alternative approach of deriving 

instream criteria for south Florida inland flowing waters outside of the lands of the 

Miccosukee and Seminole Tribes, EvPA, and EAA. Specifically, EPA requests comment 

on the scientific defensibility of this alternative approach as well as whether application 

of this approach will result in numeric nutrient criteria that protect the State’s designated 
Page 143 of 221

uses and ensure that nutrient concentrations of a body of water support balanced natural 

populations of aquatic flora and fauna. 

Commenters who submitted comments or scientific information related to 

numeric nutrient criteria for south Florida inland flowing waters during the public 

comment period for EPA’s proposed inland waters rule (75 FR 4173) should reconsider 

their previous comments in light of the new information presented in this proposal and 

must re-submit their comments during the public comment period for this rulemaking to 

receive EPA response.

F. Applicability of Criteria When Final

EPA’s proposesd that the numeric nutrient criteria for Florida’s estuaries, coastal

waters, and south Florida inland flowing waters described in this rule will be effective for 

CWA purposes 60 days after EPA publishes final criteria, and they will apply in addition 

to any other criteria for Class I, II, or Class III waters already adopted by the State and 

submitted to EPA (and for those adopted after May 30, 2000, approved by EPA). EPA 

requests comment on this proposed effective date. 

Additionally, EPA also requests comment on the alternative of a delayed effective 

date, such as the 15-month delayed effective date that EPA promulgated in the final 

inland waters rule. EPA subsequently further extended the effective date of the 2010 rule

to allow time for FDEP to finalize and EPA to review Florida’s own numeric nutrient 

criteria rulemaking and reduce any administrative confusion and inefficiency that should 

occur if Federal criteria took effect while FDEP was finalizing or EPA was reviewing the 

Comment [E35]: OMB edits accepted.
Page 144 of 221

State rulemaking. Florida’s newly-approved State WQS include a schedule for future 

State rulemaking whereby they will develop numeric nutrient criteria for additional 

estuaries by June 30, 2013 and again by June 30, 2015. If Florida is on schedule toward 

adoption of protective and approvable standards for their additional waters, EPA may 

consider delaying the effective date of its final rule to after June 30, 2015 to allow time 

for Florida to finalize and EPA to review the State’s numeric nutrient criteria.

For water bodies that Florida has designated as Class I, II, and III, any final EPA 

numeric nutrient criteria will be applicable CWA water quality criteria for purposes of 

implementing CWA programs including permitting under the NPDES program, as well 

as monitoring and assessment, and establishment of TMDLs. The proposed criteria in this 

rule, when finalized, would be subject to Florida’s general rules of applicability to the 

same extent as are other State-adopted and/or federally-promulgated criteria for Florida 

waters. Furthermore, states have discretion to adopt general policies that affect the 

application and implementation of WQS (40 CFR 131.13). There are many applications 

of criteria in Florida’s water quality programs. Therefore, EPA believes that it is not 

necessary for purposes of this proposed rule to enumerate each of them, nor is it 

necessary to restate any otherwise generally applicable requirements.

It is important to note that no existing TMDL for waters in Florida will be 

rescinded or invalidated as a result of finalizing this proposed rule, nor will this proposed 

rule when finalized have the effect of withdrawing any prior EPA approval of a TMDL in 

Florida. Neither the CWA nor EPA regulations require TMDLs to be completed or 

revised within any specific time period after a change in water quality standards occurs. 

TMDLs are typically reviewed as part of states’ ongoing water quality assessment 

Comment [E36]: Paragraph added per OMB 

request.
Page 145 of 221

programs. Florida may review TMDLs at its discretion based on the State’s priorities, 

resources, and most recent assessments. NPDES permits are subject to five-year permit

cycles, and in certain circumstances are administratively continued beyond five years. In 

practice, States often prioritize their administrative workload in permits. This 

prioritization could be coordinated with TMDL review. Because current nutrient TMDLs

were established to protect Florida's waters from the effects of nitrogen and phosphorus 

pollution, the same goal as EPA's numeric nutrient criteria, the Agency believes that, 

absent specific new information to the contrary, it is reasonable to presume that basing 

NPDES permit limits on those TMDLs will result in effluent limitations as stringent as 

necessary to meet the federal numeric nutrient criteria.

IV. Under What Conditions Will EPA Either Not Finalize or Withdraw These 

Federal Standards?

Under the CWA, Congress gave states primary responsibility for developing 

and adopting water quality standards for their navigable waters (CWA section 303(a)-

(c)). On June 13, 2012, FDEP submitted new and revised WQS for review by the EPA 

pursuant to section 303(c) of the CWA. On November 30, 2012, EPA approved the 

provisions of these rules submitted for review that constitute new or revised WQS (see 

Section II.F for additional information). Florida continues to have the option to adopt and 

submit to EPA numeric nutrient criteria for any of the State’s Class I, Class II, and Class 

III waters that are not covered in their June 13, 2012 submission to EPA, consistent with

CWA section 303(c) and implementing regulations at 40 CFR 131. Although EPA is 

proposing numeric nutrient criteria for Florida estuaries, coastal waters, and south Florida 

Comment [E37]: Sentence added per OMB 

request.
Page 146 of 221

inland flowing waters, if EPA approves criteria that are legally effective under Florida 

law for any other waters covered in this proposed rule as fully satisfying the CWA before 

publication of the final rulemaking, EPA will not proceed with the final rulemaking for 

those waters. Also, EPA will not proceed with final rulemaking for numeric DPVs, 

provided that the district court modifies the Consent Decree consistent with EPA’s

amended determination that numeric DPVs are not necessary to meet CWA requirements 

in Florida (see Section I.A for more information).

Pursuant to 40 CFR 131.21(c), if EPA finalizes this proposed rule, EPA’s 

promulgated water quality standardsWQS are become applicable water quality 

standardsWQS for purposes of the CWA on their effective date unless or until EPA 

withdraws those federally-promulgated water quality standardsWQS. Withdrawing the 

Federal standards for the State of Florida would require rulemaking by EPA pursuant to 

the requirements of the Administrative Procedure Act (5 U.S.C.551 et seq.). EPA would 

undertake such a rulemaking to withdraw the Federal criteria if and when Florida adopts 

and EPA approves numeric nutrient criteria that fully meet the requirements of section 

303(c) of the CWA and EPA’s implementing regulations at 40 CFR 131. If Florida 

adopts and EPA approves nutrient criteria that meet these requirements for a subset of 

waters, EPA would withdraw the Federal standards for that subset of waters. 

V. Alternative Regulatory Approaches and Implementation Mechanisms

A. Designating Uses

Under CWA section 303(c)(2)(A), states shall adopt designated uses after taking 

“into consideration the use and value of water for public water supplies, protection and 

propagation of fish, shellfish, and wildlife, recreation in and on the water, agricultural, 

Comment [E38]: OMB edits accepted.

Comment [E39]: OMB edit accepted.
Page 147 of 221

industrial and other purposes including navigation.” Designated uses “shall be such as to 

protect the public health or welfare, enhance the quality of water and serve the purposes 

of [the CWA].” (CWA section 303(c)(2)(A)). EPA’s regulation at 40 CFR 131.3(f) 

defines “designated uses” as “those uses specified in water quality standards for each 

water body or segment whether or not they are being attained.” A “use” is a particular 

function of, or activity in, waters of the United States that requires a specific level of 

water quality to support it. In other words, designated uses are a state’s concise 

statements of its management objectives and expectations for individual surface waters.

In the context of designating uses, states often work with stakeholders to identify 

a collective goal for their waters that the state intends to strive for as it manages water 

quality. States may evaluate the attainability of these goals and expectations to ensure 

they have designated appropriate uses (40 CFR 131.10(g)). EPA’s regulations at 40 CFR 

131 interpret and implement CWA sections 101(a)(2) and 303(c)(2)(A) to require that 

states adopt designated uses that provide water quality for the protection and propagation 

of fish, shellfish, and wildlife and for recreation in and on the water (referred to as uses 

specified in section 101(a)(2) of the Act), wherever attainable (40 CFR 131.2; 

131.5(a)(4); 131.6(a),(f); 131.10(g),(j)). Where states do not designate uses specified in 

101(a)(2) of the Act, or remove such uses, they must demonstrate that the uses are not 

attainable consistent with the use attainability analysis (UAA) provisions of 40 CFR 

131.10, specifically 131.10(g). A state may remove protection for a use specified in 

CWA section 101(a)(2) if it can show, based on a UAA consistent with 131.10, that

attaining such a designatedthe use is not attainablefeasible. States may include waters 

located in the same watershed in a single UAA, provided that there is site-specific 
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information to show how each individual water fits into the group in the context of any 

single UAA and how each individual water meets the applicable requirements of 40 CFR 

131.10(g) for removing or modifying a use. 

EPA’s proposed numeric nutrient criteria for estuaries, coastal waters, and south 

Florida inland flowing waters will apply to those waters designated by Florida as Class I 

(Potable Water Supplies), Class II (Shellfish Propagation or Harvesting), and Class III 

(Recreation, Propagation and Maintenance of a Healthy, Well-Balanced Population of 

Fish and Wildlife). If Florida removes the Class I, Class II, and/or Class III designated 

use for any particular water body ultimately affected by this rule such that it is no longer 

designated as either Class I, II, or III, and EPA approves such a removal because it is 

consistent with CWA section 303(c) and regulations at 40 CFR 131, then the federallypromulgated numeric nutrient criteria would not apply to that water body. Only the water 

quality criteria associated with the revised designated use would apply to that water body.

B. Variances

A variance may be described as a time-limited designated use and criteria that 

target a specific pollutant(s), source(s), water body(ies) and/or water body segment(s). 212

Variances constitute new or revised water quality standards subject to the procedural and

substantive requirements applicable to removing a designated use.213 Thus, EPA may 

only approve a variance if it is based on the same factors, set out at 40 CFR 131.10(g), 

that are required to revise a use specified in CWA section 101(a)(2) through a UAA.

 212 Water Quality Standards Regulation, 40 C.F.R. Part 131: Advance notice of proposed rulemaking.

USEPA Fed. Reg. 63:129 (July 7, 1998). p. 36741-36806. 213 In re Bethlehem Steel Corporation, General Counsel Opinion No. 58. March 29, 1977 (1977 WL 28245 

(E.P.A. G.C.)). USEPA. 1994. Water Quality Standards Handbook: Second Edition. EPA-823-B-94-005a. 

U.S. Environmental Protection Agency, Office of Water, Washington, DC.

Comment [E40]: OMB edits accepted.

Comment [E41]: OMB edit accepted.
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Typically, variances are time-limited, but may be renewed. Temporarily 

modifying the designated use for a particular water body through a variance process 

allows a state to identify an interim designated use and associated criteria to serve as the 

basis for NPDES permit limits and issuing certifications under CWA section 401 during 

the term of the variance while maintaining the designated use and associated criteria as 

the ultimate goal. A state should seek a variance instead of removing or revising the 

designated use where the state believes the designated use and associated criteria can be 

attained at some point in the future. By maintaining the designated use, and associated 

criteria, and by specifying a point in the future when the designated use will be fully 

applicable in all respects, the state ensures that further progress will be made in 

improving water quality and attaining the ultimate goal.

A variance may be written to address a specific geographic area, a specific

pollutant or pollutants, and/or a specific discharger. All other applicable water quality 

standards not specifically modified by the variance, including any other criteria adopted 

to protect the designated use, remain applicable. State variance procedures, as part of 

state water quality standards, must be consistent with the substantive requirements of 40 

CFR 131. Each variance must be submitted to EPA as a revised water quality standard for 

review and approval or disapproval pursuant to CWA section 303(c).

For purposes of this proposal, EPA is proposing criteria that apply to use 

designations that Florida has already established. EPA believes that the State continues to 

have sufficient authority under 131.10 to grant variances under its variance procedures to

Class I, Class II or Class III uses and associated criteria. For this reason, EPA is not 

proposing a Federal variance procedure. 

Comment [E42]: OMB edit accepted.
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C. Site-Specific Alternative Criteria

Site-specific alternative criteria (SSAC) are alternative values to otherwise 

applicable water quality criteria that would be applied on a watershed, area-wide, or 

water body-specific basis that meet the regulatory test of protecting the water’s

designated use, having a basis in sound science, and ensuring the protection and 

maintenance of downstream water quality standards. SSAC may be more or less stringent 

than the otherwise applicable criteria. In either case, because the SSAC must protect the 

same designated use and must be based on sound science according to the requirements

of 40 CFR 131.11(a), there is no need to modify the designated use or conduct a UAA. A

SSAC may be appropriate when additional scientific data and analyses can bring 

increased precision or accuracy to expressing the concentration of a water quality 

parameter that is protective of the designated use.

In EPA’s 2010 rulemaking for Florida’s lakes and flowing waters outside of the 

South Florida Nutrient Watershed Region, EPA promulgated a procedure whereby EPA’s 

Region 4 Regional Administrator may establish a SSAC after making available the 

proposed SSAC and supporting documentation for public comment (40 CFR 131.43(e)).

This procedure became effective for CWA purposes on February 4, 2011. Under this 

provision, any entity, including the State, can submit a proposed Federal SSAC directly 

to EPA for the Agency’s review and assessment as to whether an adjustment to the 

applicable Federal numeric nutrient criteria is warranted. The Federal SSAC process is 

separate and distinct from the State’s SSAC processes in its water quality standards.

The current Federal SSAC procedure allows EPA to determine that a revised sitespecific chlorophyll a, TN, TP, or nitrate+nitrite numeric criterion should apply in lieu of 
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the generally applicable criteria promulgated in the final rule for Florida’s lakes and 

flowing waters where that SSAC is demonstrated to be protective of the applicable 

designated use(s). The promulgated procedure provides that EPA will solicit public 

comment on its determination. Because EPA’s rule established this procedure, 

implementation of this procedure does not require withdrawal of the associated federallypromulgated criteria for the Federal SSAC to be effective for purposes of the CWA. EPA 

has promulgated similar procedures for EPA’s granting of variances and SSACs in other 

federally-promulgated water quality standards.

214

As outlined in 40 CFR 131.43(e) and in the draft “Technical Assistance for 

Developing Nutrient Site-Specific Alternative Criteria in Florida” (June 2011), the 

process for obtaining a Federal SSAC includes the following steps. First, an entity 

seeking a SSAC compiles the supporting data, conducts the analyses, develops the 

expression of the criterion, and prepares the supporting documentation demonstrating that 

alternative numeric nutrient criteria are protective of the applicable designated use. The 

“entity” may be the State, a city or county, a municipal or industrial discharger, a 

permittee, a consulting firm acting on the behalf of a client, or any other individual or 

organization. The entity requesting the SSAC bears the burden of demonstrating that any 

proposed SSAC meets the requirements of the CWA and EPA’s implementing 

regulations, specifically 40 CFR 131.11. Second, if the entity is not the State, the entity 

must provide notice of the proposed SSAC to the State, including all supporting 

documentation so that the State may provide comments on the proposal to EPA. Third, 

EPA’s Region 4 Regional Administrator will evaluate the technical basis and 

 214 See 40 CFR 131.33(a)(3), 40 CFR 131.34(c), 40 CFR 131.36(c)(3)(iii), 40 CFR 131.38(c)(2)(v), 40 

CFR 131.40(c).

Comment [E43]: OMB edit accepted.
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protectiveness of the proposed SSAC and decide whether to publish a public notice and 

take comment on the proposed SSAC. The Regional Administrator may decide not to 

publish a public notice and instead return the proposal to the entity submitting the 

proposal, with an explanation as to why the proposed SSAC application did not provide 

sufficient information for EPA to determine whether it meets CWA requirements or not.

If EPA solicits public comment on a proposed SSAC, upon review of comments, the 

Regional Administrator may determine that the Federal SSAC is or is not appropriate to 

account for site-specific conditions and make that determination publicly available 

together with an explanation of the basis for the decision.

Since the SSAC provision in EPA’s 2010 rule became effective, numerous 

entities have contacted EPA regarding a possible interest in obtaining a federal SSAC. 

However, following discussions with EPA, it became clear that a different water quality 

standards mechanism, such as a designated use change or variance, would be more 

appropriate in their particular situation. On March 9, 2011, EPA received a SSAC request 

from a pulp and paper mill that discharges to the Fenholloway River. Since the SSAC 

was derived from data in a nearby reference stream, the Econfina River, the TN and TP 

SSAC were requested to apply to both the Econfina and Fenholloway Rivers. Additional 

information was submitted by the requestor during 2011 and 2012 to address questions 

posed by EPA. At this time, EPA does not have sufficient information to move forward 

with proposing or establishing the TP or TN SSAC for the Fenholloway and Econfina 

Rivers.

EPA believes that there is benefit in extending this procedure for EPA adoption of 

Federal SSAC that will adjust the numeric nutrient criteria proposed in this rule. EPA is 

Comment [E44]: Paragraph added per OMB 

request.
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therefore proposing that a similar procedure promulgated in 40 CFR 131.43(e) apply to 

estuaries, coastal waters, and south Florida inland flowing waters. EPA requests comment

on the following proposed application of the SSAC procedure.

To successfully develop a Federal SSAC for a given estuary, coastal water, or 

south Florida inland flowing water, a thorough analysis is necessary that indicates how 

the alternative concentration of TN, TP, or chlorophyll a supports both the designated 

use(s) of the water body itself, and provides for the attainment and maintenance of the 

WQS of downstream water bodies, where applicable. This analysis should have 

supporting documentation that consists of examining indicators of longer-term response 

to multiple stressors, such as seagrass health, as well as indicators of shorter-term 

response specific to nitrogen and phosphorus pollution, such as chlorophyll a 

concentrations associated with balanced phytoplankton biomass or sufficient dissolved 

oxygen to maintain aquatic life.

EPA is proposing seven approaches for developing SSAC for estuaries, coastal

waters, and south Florida inland flowing waters that are similar to the four approaches 

EPA finalized in the 2010 rule for Florida’s lakes and flowing waters. The first five 

proposed approaches are replicating the approaches EPA used to develop estuary, tidal 

creek, marine lake, coastal, and south Florida inland flowing water criteria, respectively, 

and applying these methods to a smaller subset of waters or water body segments. To 

understand the necessary steps in this analysis, interested parties should refer to the 

complete documentation of these approaches in the Technical Support Document for this 

proposed rule.

Comment [E45]: OMB edit accepted.
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The sixth proposed approach for developing SSAC is to conduct a biological, 

chemical, and physical assessment of water body conditions. A detailed description of the 

supporting rationale must be included in the documentation submitted to EPA. The 

components of this approach could include, but are not limited to, evaluation of: seagrass 

health, presence or absence of native flora and fauna, chlorophyll a concentrations or 

phytoplankton density, average daily dissolved oxygen fluctuation, organic versus 

inorganic components of total nitrogen, habitat assessment, and hydrologic disturbance.

This approach could apply to any water body type, with specific components of the 

analysis tailored for the situation.

The proposed seventh approach for developing SSAC is a general provision for 

using another scientifically defensible approach that is protective of the designated use.

This provision allows applicants to make a complete demonstration to EPA using 

methods not otherwise described in the rule or its statement of basis, consistent with 40 

CFR 131.11(b)(1)(iii). This approach could potentially include use of mechanistic models 

or other data and information.

D. Compliance Schedules

A compliance schedule, or schedule of compliance, refers to “a schedule of 

remedial measures included in a ‘permit,’ including an enforceable sequence of interim 

requirements ... leading to compliance with the CWA and regulations.” (40 CFR 122.2, 

CWA section 502(17)). In an NPDES permit, Water Quality-Based Effluent Limitations 

(WQBELs) are effluent limits based on applicable water quality standards for a given 

pollutant in a specific receiving water (NPDES Permit Writers Manual, EPA-833-B-96-

003, December, 1996). EPA regulations provide that schedules of compliance may only 
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be included in permits if they are determined to be “appropriate” given the circumstances 

of the discharge and are to require compliance “as soon as possible” (40 CFR 122.47).215

Florida has adopted a regulation authorizing compliance schedules. That 

regulation, Subsection 62-620.620(6), F.A.C., is not affected by this proposed rule. The 

complete text of the Florida rules concerning compliance schedules is available at 

https://www.flrules.org/gateway/RuleNo.asp?ID=62-620.620. Florida is, therefore, 

authorized to grant compliance schedules, as appropriate, under its rule for WQBELs 

based on EPA’s federally-promulgated numeric nutrient criteria.

VI. Economic Analysis

The CWA provides a comprehensive framework for the protection and 

restoration of the health of the Nation’s waters. EPA determined in 2009 that addressing 

the significant number of Florida waters impaired by nitrogen and phosphorus required 

the establishment of numeric nutrient criteria as part of Florida water quality standards 

adopted under the CWA. State implementation of numeric nutrient criteria in the 

proposed rule may result in an incremental level of controls needed for compliance with 

CWA programs, or require them sooner than would occur under current CWA programs. 

These controls include new or revised National Pollutant Discharge Elimination System 

(NPDES) permit conditions for point source dischargers and controls on other sources of 

nitrogen and phosphorus (e.g., agriculture, urban runoff, and septic systems) through the 

development of Total Maximum Daily Loads (TMDLs) and Basin Management Action 

Plans (BMAPs). 

 215 Hanlon, Jim. USEPA Office of Wastewater Management. 2007, May 10. Memorandum to Alexis 

Stauss, Director of Water Division EPA Region 9, on “Compliance Schedules for Water Quality-Based 

Effluent Limitations on NPDES Permits.”
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EPA conducted an analysis to estimate both the increase in the number of 

impaired waters that may be identified as a result of the proposed rule, and the potential 

annual cost of CWA pollution control actions likely to be implemented by the State of 

Florida and private parties to assure attainment of applicable State water quality 

designated uses. It is important to note that the costs of pollution controls needed to attain 

water quality standards for nutrients for waters already identified as impaired by the State 

(including waters with and without TMDLs in place) are not included in EPA estimates 

of the cost of the rule. EPA’s analysis is fully described in the document entitled 

Economic Analysis of Proposed Water Quality Standards for the State of Florida’s 

Estuaries, Coastal Waters, and South Florida Inland Flowing Waters (hereinafter 

referred to as the Economic Analysis), which can be found in the docket and record for 

this proposed rule. This analysis shows that the incremental costs associated with the 

proposed rule range between $239.0 million and $632.4 million per year (2010 dollars) 

and monetized benefits may be in the range from $39.0 to $53.4 million annually.

1. NRC Review of Phase 1 Cost Estimates

On December 6, 2010 EPA published a final rule to set numeric nutrient criteria 

for lakes and streams in Florida designed to protect those waters for their Statedesignated uses, such as swimming, fishing, or as drinking water sources (Phase 1 rule). 

EPA developed an economic analysis to provide the public with information on potential 

costs and benefits that may be associated with Florida’s implementation of EPA’s rule. 

EPA’s estimate of the annual costs of that rule ranged from $135.5 to $206.1 million; 

stakeholder estimates of the same cost categories ranged from $8 to $13 billion annually. 

While these costs are not directly related to today’s proposed rule, EPA determined that 
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an independent peer review of its economic analysis for the Phase 1 rule would provide 

important information on the disparity between EPA’s cost estimates and those of some 

stakeholders, and would be helpful to inform and improve its analysis of today’s 

proposed rule. Accordingly, EPA requested the National Research Council (NRC) of the 

National Academies to review EPA’s economic analysis for the Phase 1 rule. The NRC

Committee completed its “Review of the EPA’s Economic Analysis of Final Water 

Quality Standards for Nutrients for Lakes and Flowing Waters in Florida” in June. The 

Committee was charged with reviewing and commenting on three specific areas: 

1) EPA’s assumption that only newly impaired waters should be analyzed,

2) EPA’s decision to estimate costs associated only with sources affecting newly 

impaired waters, by sector, and

3) EPA’s assumptions about levels of control by point and nonpoint sources, 

including the use of variances and other flexibilities for more cost-effective 

approaches and whether to implement reverse osmosis and other stringent control 

technologies.

NRC answered the first charge, agreeing with EPA’s assumption that only newly 

impaired waters should be analyzed. NRC also addressed the second charge, but took 

exception with EPA’s approach to not estimating costs for unassessed waters or for septic 

systems affecting impaired springsheds. NRC also suggested that EPA underestimated 

the affected acres in agriculture. The Committee did not offer specific suggestions for 

how to compute the increased acreage that should be analyzed. However, on the cost 

side, they suggest including costs associated with installation of regional treatment 

systems on agricultural lands.
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As for the third charge, the Committee largely addressed this by examining the 

details of EPA’s unit costs, including comments suggesting ways in which EPA 

underestimated or overestimated costs. The Committee did not directly address EPA’s 

assumptions regarding the use of SSACs, variances and use designations, except to 

propose an alternative cost estimating framework based on predicting the future time path 

of waters progressing through the stages of listing as impaired, TMDL development, and 

BMAP implementation, with and without the rule. The Committee generally concluded 

that EPA’s cost estimates were likely too low, while the stakeholder estimates were too 

high.

In response to the NRC review, EPA has attempted to incorporate many of the 

recommendations and suggestions made throughout the NRC report including: using the 

HUC-12 watershed unit of analysis; analyzing potential costs for unassessed waters that 

could be incrementally impaired; analyzing costs for each industrial plant rather than 

extrapolating the results from a small sample; reviewing actual experience from existing 

TMDLs to identify BMPs sufficient to meet numeric targets; considering permeable 

reactive barriers for septic systems and their installation costs; and considering 

uncertainty in government expenditures. EPA has addressed these recommendations and 

suggestions in this analysis of costs for the coastal and estuary criteria.

The NRC Committee also described an approach for EPA to consider in analyzing 

the impacts of its numeric nutrients criteria rules by tracing out two time-paths of costs 

and benefits: one time-path for the baseline and one reflecting the proposed rule. The 

costs and benefits of the proposed rule could then be analyzed as the present value of the 

difference in the two time-paths of costs and benefits, respectively. To execute this 
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approach, EPA would need to model not just its projection of the eventual controls that 

would be implemented under the proposed rule, but its predictions of the prioritization of 

watersheds that Florida would adopt to determine the timing of controls. NRC suggested 

that EPA could engage external stakeholders in a collaborative process to determine a 

collective set of assumptions to use as part of this analytical approach (or at least to 

“isolate and possibly reconcile” areas of disagreement). EPA acknowledges the merit of 

this approach, and notes that it is consistent with EPA’s intent that its numeric nutrients 

criteria simply interpret Florida’s current narrative nutrient criterion, by providing the 

often time-consuming first step of the science-based modeling necessary for developing a 

TMDL. The ultimate effect of the EPA’s proposal would be to improve the efficiency 

and effectiveness of Florida’s WQS program with regard to nutrients. However, given 

the exigencies of the consent decree and the timing of the NRC review, EPA determined 

that it was not possible to adopt the NRC’s alternative approach for this proposal. The 

NRC’s alternative approach was presented as a finding, rather than a recommendation, 

because the NRC acknowledged that time and budget constraints might render this 

approach unworkable for the current rule.

Considering the exigencies, EPA took the approach of estimating costs and 

benefits for a representative future year, using current water quality data as a basis for 

projecting what incremental water quality controls would need to be implemented during 

this future year to meet the new criteria. An approach that compares two complete future 

time-paths (with and without the proposed rule) requires taking the difference between 

those two time-paths, discounting over time, and summing in order to express the impacts 

in present value terms. In contrast, EPA’s approach identifies waters that would be 
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newly identified as impaired and the controls that would be needed to meet the new 

criteria. EPA then annualizes the costs of these controls over an appropriate time 

horizon. As such, the two approaches are not directly comparable. Nonetheless, EPA 

believes its approach sheds light on the costs and benefits associated with its numeric 

nutrients criteria rules and complies with the Executive Order requirements for 

conducting economic analysis of regulations. As noted above, EPA has made significant 

changes to its approach to address the NRC recommendations that are applicable to it.

2. Baseline for Cost Analysis

EPA is promulgating numeric nutrient criteria to supplement the State of Florida’s 

current narrative nutrient criteria. The incremental impacts of the proposed rule are the 

potential costs and benefits associated with implementation of the proposed numeric 

criteria, including DPVs, for estuaries, coastal waters, and south Florida inland flowing 

waters, above and beyond the costs associated with State implementation of its current 

narrative nutrient criterion. The baseline incorporates requirements associated with 

restoration of already identified impaired waters, including waters for which TMDLs are 

approved and waters for which TMDLs are not yet developed. Because the numeric 

nutrients criteria proposed here interpret Florida’s existing narrative criterion, which is 

also the basis for existing TMDLs, the analysis assumes that these TMDLs would be 

adopted as site-specific criteria. Thus, there would be no additional costs or benefits 

associated with the proposed rule for these waters. The baseline for this analysis also 

includes EPA’s previously promulgated numeric nutrient criteria for Florida’s lakes and 

flowing waters. 
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For waters that the State of Florida has already identified as impaired but for 

which it has not yet developed TMDLs, EPA expects that the effect of this proposed rule 

will be to shorten the time and reduce the resources necessary for the State of Florida to 

develop TMDLs and BMAPs. For waters that the State of Florida has developed 

TMDLs, EPA has looked at the proposed criteria to compare these to the target loadings 

in the TMDLs and has not found a consistent pattern of existing TMDLs being either 

more or less stringent than would be required to meet the criteria proposed in this rule. 

For already impaired waters and waters already under a TMDL, EPA assumed that no 

additional controls on nonpoint sources to these waters would be needed as a 

consequence of this rule. However, there may be an incremental impact of the proposed 

rule for any point source dischargers to these waters that have or may receive waste load 

allocations for just one nutrient pollutant if those waters are not attaining criteria for the 

other as a result of this proposed rule. These costs are included in this economic analysis. 

For waters not currently impaired under the baseline, EPA uses current water 

quality measurements to predict which waters would be deemed unimpaired as a result of 

the proposed rule (and therefore need not be analyzed for nonpoint source control costs). 

EPA acknowledges that these conditions could change in the future. To the extent that 

the experience in implementation of the proposed rule deviates from these specific 

assumptions about the baseline, EPA’s estimates of the costs and benefits may be underor overestimated. See Section 2 of the Economic Analysis for a full description of the 

baseline. EPA requests comment on its assumptions regarding the baseline. 

3. Incremental Costs
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The likely effect of this proposed rule will be the assessment and identification of 

additional waters that are impaired and not meeting the numeric water quality criteria in 

the proposed rule. The incremental impact of the proposed rule includes the costs for 

controls on point and nonpoint sources, developing and implementing TMDLs to attain 

the proposed criteria, and the monetary value (benefits) of the resulting potential increase 

in water quality. The economic analysis describes these potential incremental impacts of 

the proposed rule. It is important to note that EPA took care not to include costs for the

estuarine and coastal marine waters contained in Florida’s newly-approved State WQS.

To develop these estimates, EPA first assessed State control requirements 

associated with current water quality, existing impaired waters, and existing TMDLs, as 

well as existing regulations specific to estuaries, coastal waters and south Florida inland 

flowing waters (the baseline). EPA then identified the costs and benefits associated with 

additional pollution controls to meet EPA’s proposed numeric criteria, beyond pollution 

controls currently needed or in place. To estimate incremental costs to municipal and 

industrial dischargers, EPA gathered publicly available facility information and data on 

potential control technologies, and used Florida Department of Environmental Protection 

(FDEP) point source implementation procedures to estimate the change in WQBELs and 

treatment controls that could result from the proposed rule. EPA assessed potential nonpoint source control costs by using publicly available information and data to determine 

land uses near waters that would likely be identified as impaired under the proposed rule. 

EPA used current FDEP data on stormwater controls and Florida Department of 

Agricultural and Consumer Services (FDACS) manuals to estimate costs of 

implementing stormwater and agricultural best management practices (BMPs) to attain 
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the proposed numeric criteria. EPA also estimated the potential costs associated with 

upgrades of homeowner septic systems and potential government costs of developing 

additional TMDLs for water identified as impaired under this rule. Finally, EPA 

qualitatively and quantitatively described and estimated some of the potential benefits of 

complying with the new water quality standards. Although it is difficult to predict with 

certainty how the State of Florida will implement these new water quality standards, the 

result of this analysis represent EPA’s best estimates of costs and benefits of the State of 

Florida’s likely actions to implement this proposed rule. 

A. Incrementally Impaired Waters

Compared to current conditions, potentially incrementally impaired waters are 

those waters that exceed EPA’s proposed criteria for which FDEP has not already 

developed a TMDL or listed as impaired for nutrients. To estimate incremental costs 

associated with attainment of criteria, EPA first removed any waters for which the State 

of Florida has already determined to be impaired or established a TMDL and/or BMAP, 

because it considers these waters part of the baseline for this analysis. BMAPs are 

iterative and are updated on a continual basis until the TMDL targets are met. EPA 

assumes that controls will be implemented through these mechanisms until the TMDLs 

are met. Although additional costs to address baseline impairments may be needed in the 

future (after this rule is promulgated), EPA does not believe that these costs should be 

attributed to this proposed rule, but are instead part of the baseline. As discussed above, 

the State of Florida is not required to revise any existing TMDL as a result of this rule, 

and WQBELs in NPDES permits that are consistent with an existing EPA approved 

TMDL meet the requirements of the CWA. TMDL nutrient criteria have been shown to 
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be both more stringent and less stringent when compared to criteria under this proposed 

rule and EPA has provided SSACs as a mechanism to approve the standards in existing 

TMDLs and BMAPs. Thus, EPA does not anticipate that this rule will result in increased 

nonpoint source controls costs for watersheds that already have an EPA-approved 

TMDL. 

After excluding waters already identified as impaired under Florida’s existing 

narrative criteria, EPA next identified estuarine and coastal segments that do not meet the 

numeric criteria of this proposed rule. EPA then assumed identified waterbodies 

(WBIDs216) that overlap those segments may be identified as incrementally impaired. 

EPA then identified the watersheds that contain or surround, in the case of coastal waters, 

those incrementally impaired WBIDs. 

EPA analyzed FDEP’s database of ambient water quality monitoring data and 

compared monitoring data for each segment with EPA’s proposed criteria for TN and TP 

to identify incrementally impaired waters. EPA compiled the most recent five years of 

monitoring data and determined if there was sufficient data available to calculate more 

than one annual geometric mean in a consecutive three year period. With sufficient data, 

EPA calculated the annual geometric mean for each segment identified by EPA segment 

boundaries, and identified waters as incrementally impaired if they exceeded the 

applicable criteria in this proposed rule. The results of this analysis are shown in Table 

VI(A).

Table VI(A)(1): Number of WBIDs Summary of Data Analysis for Proposed Criteria1

Criteria Type Baseline 

Impaired2

Not Currently Impaired Under the 

Baseline Total

 216 WBID is a waterbody identification number assigned by Florida, in order to delineate the boundaries of 

Florida’s waters.
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Data Available3 Data Not Available

Coastal 0 5 68 73

Estuaries 42 121 95 258

Total 42 126 163 331

Source: FDEP IWR run 44.

1. Represents number of WBIDs, based on 10% of WBID area overlapping segments for which EPA is 

proposing numeric nutrient criteria.

2. On 303(d) list as impaired for nutrients or covered under a nutrient-related TMDL. EPA did not assess 

these waters further for attainment of the proposed criteria.

3. WBIDs in segments for which at least two geometric means in a consecutive three year period can be 

calculated based on having at least four samples in a given year, with one sample in winter and summer.

Controls may also be needed to meet the proposed criteria in a portion of the 163 

WBIDs for which EPA does not have data if subsequent data would indicate impairment.

These 163 WBIDs are variously located in the same watersheds as WBIDs that are 

baseline impaired or incrementally impaired by this proposed rule, or in watersheds either 

with no known impaired WBIDs or for which none of the WBIDs have sufficient data to 

determine impairment status. Without additional information about these waters, EPA 

determined the number of impaired-though-unassessed waters as a range. As a low 

estimate, it is possible that none of the unassessed waters would be impaired. Given the 

targeting scheme for Florida’s IWR data, these unassessed waters likely have a lower 

probability of impairment than assessed waters, and zero represents the lower bound. For 

the high end of the range, EPA considered a proportional impairment rate of assessed 

waters. The impairment rate of unassessed waters may be anywhere in between.

While helpful in establishing the number of waterbodies that may be 

incrementally impaired, the assumption of proportional impairment does not produce 

information on location needed to estimate associated costs. The majority of unassessed 

waters lie along the coast and in close proximity to baseline impaired and impaired 

assessed waters. Hence, for this analysis, EPA assumed that impairment in unassessed 

waters would most likely be near baseline impairments and impaired assessed waters, 
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since the loads causing impairment in these assessed waters could also affect the 

downstream unassessed waters. For coastal waters and south Florida waters, EPA used

GIS to locate waters within or adjacent to the same watersheds associated with baseline 

impairments and impaired assessed waters. For estuaries, the number of unassessed 

waters estimated to be impaired (based on the assumption of proportional impairment) 

would not fit within the same watersheds associated with baseline impairments and 

impaired assessed waters. Therefore, EPA used GIS analysis to identify a buffer around 

the watersheds associated with baseline impairments and impaired assessed waters that 

would just include the estimated number of impaired unassessed waters. EPA found that 

a buffer size of 0.7 miles encompassed the estimated number of impaired unassessed 

waters. A smaller buffer (e.g., 0.5 mile) would not include enough unassessed waters. A 

larger buffer (e.g., 1 mile) would include too many unassessed waters. EPA then used 

this 0.7 mile buffer to identify the associated incremental watersheds that may need 

nonpoint source controls. EPA has estimated the acres of various land uses within these 

watersheds and reported as the upper bound in the Additional Unassessed Water column 

of Table VI(A)(2). 

Table VI(A)(2): Summary of Land Use in Incrementally Impaired Watersheds for the Analysis 

of Costs under the Proposed Rule (acres)

Land Use Type Assessed Waters1 Additional 

Unassessed Water2 Total

Agriculture 15,312 0 - 22,828 15,312 - 38,140

Communications and Utilities 3,337 0 - 3,315 3,337 - 6,652

Forest 199,432 0 - 256,137 199,432 - 455,569

Industrial 2,025 0 - 6,703 2,025 - 8,729

Other 9,276 0 - 11,306 9,276 - 20,582

Transportation Corridors 9,177 0 - 3,636 9,177 - 12,813

Urban 128,787 0 - 86,508 128,787 - 215,295

Water 220,728 0 - 102,615 220,728 - 323,343
Page 167 of 221

The costs associated with the additional controls that would be necessary in the 

watersheds not already included in the cost analysis because of known incremental 

impaired waters will be included in the remainder of this section.

B. Point Source Costs

Point sources of wastewater must have a National Pollution Discharge 

Elimination System (NPDES) permit to discharge into surface waters. EPA identified 

point sources potentially discharging nitrogen and phosphorus to estuaries, coastal 

waters, and south Florida inland flowing waters by evaluating the Integrated Compliance 

Information System-National Pollutant Discharge Elimination System (ICIS-NPDES) 

database. EPA identified all facilities with any permitted discharge to estuarine, coastal, 

and south Florida inland flowing waters with an existing effluent limit or monitoring 

requirement for nitrogen or phosphorus, as well as those with the same industry code as 

any point source with an identified nutrient monitoring requirement. This analysis 

identified 121 point sources as having the potential to discharge nitrogen and/or 

phosphorus. Table VI(B) summarizes the number of point sources with the potential to 

discharge nitrogen and/or phosphorus.

Wetlands 196,545 0 - 322,355 196,545 - 518,899

Total 784,619 0 - 815,403 784,619 - 1,600,022

1. Total acreage of 12-digit HUC watersheds surrounding the incrementally impaired WBIDs based on 

sufficient data, excluding watersheds for which EPA has already estimated a need for controls.

2. Acreage surrounding potential incrementally impaired unassessed waters not associated with 

baseline impairment or incremental impairment under the proposed rule based on sufficient data.
Page 168 of 221

Table VI(B). NPDES-Permitted Wastewater Dischargers Potentially Affected by 

Proposed Rule

Discharger Category Major Dischargers a Minor Dischargers b Total

Municipal Wastewater 53 31 84

Industrial Wastewater 19 18 37

Total 72 49 121 a Facilities discharging greater than one million gallons per day or likely to discharge toxic pollutants in 

toxic amounts. 

b Facilities discharging less than one million gallons per day and not likely to discharge toxic pollutants in 

toxic amounts.

1. Municipal Waste Water Treatment Plant (WWTP) Costs

EPA considered the costs of known nitrogen and phosphorus treatment options 

for municipal WWTPs. Nitrogen and phosphorus removal technologies that are available 

can reliably attain annual average total nitrogen (TN) concentration of approximately 

3.0 mg/L or less and annual average total phosphorus (TP) concentration of 

approximately 0.1 mg/L or less.217 EPA considered wastewater treatment to these 

concentrations to be the target levels for the purpose of this analysis. The NRC suggested 

that there is uncertainty associated with this assumption because dischargers to impaired 

waters typically receiving WQBELs equal to the numeric water quality criteria (NRC, 

2012; p. 48). However, procedures for determining appropriate WQBELs include an 

evaluation of effluent quality and assimilative capacity of the receiving water. 

Specifically for nutrients, EPA found no implementation evidence in Florida to support 

the assumption that the criteria would be adopted as end-of-pipe limits. Instead, based on 

the State of Florida protocol218 and the examples from existing nutrient TMDLs, EPA 

 217 U.S. EPA, 2008, “Municipal Nutrient Removal Technologies Reference Document. Volume 1 –

Technical Report,” EPA 832-R-08-006.

218 Florida Department of Environmental Protection (FDEP). 2006a. TMDL Protocol. Version 6.0. Task 

Assignment 003.03/05-003.
Page 169 of 221

assumed for this analysis that state implementation of the proposed rule will not result in 

criteria end-of-pipe effluent limitations for municipal WWTPs.

The NPDES permitting authority determines the need for WQBELs for point 

sources on the basis of determining their reasonable potential to exceed water quality 

criteria. To determine reasonable potential on a facility-specific basis, data such as 

instream nutrient concentrations and low flow conditions would be necessary. However, 

because most WWTPs are likely to discharge nutrients at concentrations above applicable 

TN and/or TP criteria, EPA assumed that all WWTPs have reasonable potential to exceed 

the numeric criteria. The NRC supported this assumption. 

For municipal wastewater, EPA estimated costs to reduce effluent concentrations 

to 3 mg/L or less for TN and 0.1 mg/L or less for TP using advanced biological nutrient 

removal (BNR). Although reverse osmosis and other treatment technologies may have 

the potential to reduce nitrogen and phosphorus concentrations even further, EPA 

believes that implementation of reverse osmosis applied on such a large scale has not 

been demonstrated.219 The NRC supported this assumption (NRC, 2012; p. 46) but said 

that in some instances, treatment to levels beyond the controls of advanced BNR would 

be required (NRC, 2012; p. 48). Such levels have not been required for WWTPs by the 

State of Florida in the past, including for those WWTPs under TMDLs with nutrient 

targets comparable to the criteria in this proposed rule. EPA believes that should state-ofthe-art BNR technology, together with other readily available and effective physical and 

chemical treatment (including chemical precipitation and filtration), fall short of 

compliance with permit limits associated with meeting the new numeric nutrient criteria, 

 219 Treatment using reverse osmosis also requires substantial amounts of energy and creates disposal issues 

as a result of the large volume of concentrate generated.
Page 170 of 221

then it is reasonable to assume that entities would first seek out alternative compliance 

mechanisms such as reuse, site-specific alternative criteria, variances, and designated use 

modifications. In addition, under a TMDL, FDEP could allocate greater load reductions 

to nonpoint sources based on baseline contributions and existing controls, thus resulting 

in fewer reductions required from point source dischargers. EPA acknowledges that if its 

assumptions about the availability of reuse, SSACs, variances and designated use 

changes are incorrect, then the costs presented here are underestimates.

To estimate compliance costs for WWTPs, EPA identified current WWTP 

treatment capabilities using FDEP’s Wastewater Facility Regulation (WAFR) database, 

and information obtained from NPDES permits and/or water quality monitoring reports. 

Table VI(B)(1) summarizes EPA’s best estimate of the number of potentially affected 

municipal WWTPs that may require additional treatment for nitrogen and/or phosphorus 

to meet the numeric criteria supporting State designated uses.

Table VI(B)(1). Summary of Potential for Additional Nutrient Controls for Municipal Wastewater 

Treatment Plants a

Discharge 

Type

Number of Dischargers

Additional 

Reduction in 

TN and TP a

Additional 

Reduction in 

TN Only b

Additional 

Reduction in 

TP Only c

No incremental 

controls needed 

d

Total

Major 7 0 22 22 51

Minor 17 0 1 10 28

Total 24 0 23 32 79

Source: Based on treatment train descriptions in FDEP’s Wastewater Facility Regulation database220

and permits, WLAs in TMDLs and existing regulations, assuming dischargers would have to install 

advanced BNR for compliance under the rule.

a. Includes dischargers without treatment processes capable of achieving the target levels or existing 

WLA for TN and TP, or for which the treatment train description is missing or unclear. 

b. Includes dischargers with chemical precipitation only.

c. Includes dischargers with Modified Ludzack-Ettinge (MLE), four-stage Bardenpho, and BNR 

specified to achieve less than 3 mg/L, or those with WLA under a TMDL for TN only.

d. Includes dischargers with anaerobic-anoxic oxidation (A2

/O), modified Bardenpho, modified 

 220 Florida Department of Environmental Protection (FDEP). 2009. Wastewater Facility Information: 

Wastewater Facility Regulation (WAFR) database. 

http://www.dep.state.fl.us/water/wastewater/facinfo.htm. Accessed June 2009.
Page 171 of 221

University of Cape Town (UCT), oxidation ditches, or other BNR coupled with chemical precipitation, 

those with WLAs under a TMDL for both TN and TP, those discharging to waters on the 303(d) list for 

nutrients or DO, and those ocean dischargers covered under the Grizzle-Figg Act that will cease 

discharge completely by 2025.

An EPA study provides unit cost estimates for BNR for various TN and TP 

performance levels221. To estimate costs for WWTPs, EPA used the average capital and 

average operation and maintenance (O&M) unit costs for technologies that achieve an 

annual average of 3 mg/L or less for TN and/or 0.1 mg/L or less for TP. NRC noted that 

these unit costs were significantly lower than those estimated by the Florida Water 

Environment Association Utility Council (FWEAUC) and suggested to verify the unit 

costs against FWEAUC’s unit costs. Multiplying these unit costs by facility flow 

reported in EPA’s PCS database, EPA estimated that total costs could be approximately 

$44.1 million per year (2010 dollars).222

EPA also conducted a sensitivity analysis to address the potential for dischargers 

under TMDLs that establish WLAs for TN or TP (and not both pollutants), such that 

incremental costs could be required under the proposed rule to control the other pollutant. 

The results of this analysis suggest a range of additional costs from $3.6 million to $5.6

million annually (see section 5.3 of the Economic Analysis). Thus, estimated total cost 

could range from approximately $47.7 million to $49.7 million per year.

 221 USEPA. 2008. Municipal Nutrient Removal Technologies Reference Document. Volume 1 – Technical 

Report. EPA 832-R-08-006. U.S. Environmental Protection Agency, Office of Wastewater Management, 

Municipal Support Division.

222 Estimated capital costs annualized at 7% over 20 years, plus estimated annual O&M.
Page 172 of 221

2. Industrial Point Source Costs

Incremental costs for industrial dischargers are likely to be facility-specific and 

depend on process operations, existing treatment trains, and composition of waste 

streams. EPA identified 36 industrial dischargers potentially affected by the proposed 

rule. Of those, 4 are subject to an existing nutrient TMDL, and 4 discharge to waters 

currently listed as impaired. As with WWTPs, EPA assumed that costs to industrial 

dischargers under an existing nutrient TMDL with WLAs for both nitrogen and 

phosphorus and costs at facilities discharging to currently impaired waters are not 

attributable to this proposed rule because those costs would be incurred absent the rule 

(under the baseline). 

To estimate potential costs to the remaining 28 potentially affected industrial 

facilities (Table VI(B)(2)), EPA used effluent data for flows, TN, and TP from Discharge 

Monitoring Reports in EPA’s ICIS-NPDES database and other information in NPDES 

permits to determine whether or not they have reasonable potential to cause or contribute 

to an exceedance of the proposed criteria in this proposed rule. Because the numeric 

nutrient criteria are annual geometric means, EPA assumed that any discharger with an 

average TN or TP concentration greater than the proposed criterion would have 

reasonable potential. For those facilities with reasonable potential, EPA further analyzed 

their effluent data and estimated potential revised water quality based effluent limits 

(WQBELs) for TN and TP. If the data indicated that the facility would not be in 

compliance with the revised WQBEL, EPA estimated the additional nutrient controls 

those facilities would likely implement to allow receiving waters to meet designated uses 

and the costs of those controls. Although reverse osmosis and other treatment 
Page 173 of 221

technologies have the potential to reduce nitrogen and phosphorus concentrations even 

further, EPA believes that implementation of reverse osmosis applied on such a large 

scale has not been demonstrated as likely or necessary.223 If BNR or other more 

conventional cost-effective treatment technologies would not meet the revised WQBELs, 

EPA believes it is reasonable to assume that entities would first seek out other available 

compliance mechanisms such as reuse, site-specific alternative criteria, variances, and 

designated use modifications. In addition, under a TMDL FDEP could allocate greater 

load reductions to nonpoint sources based on baseline contributions resulting in fewer 

reductions from point source dischargers.

Using this method, EPA estimated that the potential costs for industrial 

dischargers could be approximately $15.2 million annually (2010 dollars). Note that a 

number of the dischargers would not incur incremental costs, while others would incur 

costs of implementing controls such as chemical precipitation, filtration, and/or BNR. 

NRC said that the use of similar unit costs for industrial flows as EPA had used for 

municipal waste water treatment facilities did not capture the higher costs associated with 

lower flows and therefore industrial costs are underestimated. The source EPA used to 

find unit costs included plant costs with low flows that EPA was able to compare to plant 

costs with high flows, as NRC suggested. EPA found no pattern for higher or lower costs 

and therefore did not change its unit costs. The NRC also suggested EPA should include 

costs for flow equalization atsome industrial facilities. EPA does not have enough flow 

data to estimate flow equalization costs, but did use the 90th percentile flows as the basis 

for costs for dischargers with variable flows (see Cost Calculations for Industrial 

 223 Treatment using reverse osmosis also requires substantial amounts of energy and creates disposal issues 

as a result of the large volume of concentrate that is generated.
Page 174 of 221

Dischargers). EPA considers the use of the 90th percentile flow together with an 

allowance for contingencies to provide sufficient costs allowance to cover the cost of 

equalization should that be necessary at individual facilities.

Table VI(B)(2): Potential Incremental Costs for Industrial Dischargers a

Industrial Category Total Number of 

Facilities

Number of 

Facilities with 

costs b

Total Annual Costs 

(million 2010$/yr)

Chemicals and Allied 

Products 1 0 $0.0

Electric Services 8 2 $0.5

Food 2 1 $0.2

Mining 0 0 $0.0

Other 14 1 $0.0

Pulp and Paper 3 3 $14.5

Total 28 7 $15.2

a May not add due to rounding

b In most cases, only a few facilities are projected to incur costs; others do not.

C. Non-point Source Costs

To estimate the potential incremental costs associated with controlling nitrogen 

and phosphorus pollution from non-point sources, EPA identified land areas near 

incrementally impaired waters using GIS analysis. EPA identified the 12-digit hydrologic 

units (HUC-12s) in Florida that contain, or in the case of coastal waters, surround an 

incrementally impaired WBID (WBIDs are GIS polygons for water assessment), and 

excluded those HUC-12s that are included in the baseline or cost analysis for in the 

Inland Rule. EPA then identified all the 12-digit HUCs that drain to any remaining 

unassessed WBIDs that may become incrementally impaired should they be assessed in 

the future. EPA then identified land uses in these HUCs using GIS analysis of data 

obtained from the State of Florida. By using the HUC-12 delineation, EPA has addressed 
Page 175 of 221

the NRC recommendation that EPA use the more refined HUC-12 delineation instead of 

the larger HUC-10 delineation. 

1. Costs for Urban Runoff

EPA’s GIS analysis indicates that urban land (excluding land for industrial uses 

covered under point sources) accounts for approximately 128,800 acres to 215,300 acres 

of the land near incrementally impaired waters. EPA’s analysis indicates that urban 

runoff is already regulated on a portion of this land under EPA’s stormwater program 

requiring municipal separate storm sewer system (MS4) NPDES permits. Florida has a 

total of 27 large (Phase I) permitted MS4s serving greater than 100,000 people and 132 

small (Phase II) permitted MS4s serving fewer than 100,000 people. MS4 permits 

generally do not have numeric nutrient limits, but instead rely on implementation of 

BMPs to control pollutants in stormwater to the maximum extent practicable. Even those 

MS4s in Florida discharging to impaired waters or under a TMDL currently do not have 

numeric limits for any pollutant.

In addition to EPA’s stormwater program, several existing State rules are intended 

to reduce pollution from urban runoff and were included in the baseline for EPA’s 

proposed rule. For example, Florida's Urban Turf Fertilizer rule (administered by 

FDACS) requires a reduction in the amount of nitrogen and phosphorus that can be 

applied to lawns and recreational areas. Florida’s 1982 stormwater rule (Chapter 403 of 

Florida statues) requires stormwater from new development and redevelopment to be 

treated prior to discharge through the implementation of BMPs. The rule also requires 

that older systems be managed as needed to restore or maintain the beneficial uses of 

waters, and that water management districts establish and implement other stormwater 
Page 176 of 221

pollutant load reduction goals. In addition, the “Water Resource Implementation Rule” 

(Chapter 62-40, F.A.C.) establishes that stormwater design criteria adopted by FDEP and 

the water management districts shall achieve at least 80% reduction of the average annual 

load of pollutants that cause or contribute to violations of water quality standards (95% 

reduction for outstanding natural resource waters). This rule sets design criteria for new 

development that is not based on impairment status of downstream waters. For NPDES 

permits, reasonable potential exists for any effluent concentrations above the criteria even 

if the water is attaining standards. Therefore, EPA assumed that post-1982 developed 

land already has controls to meet 80% reductions and only older developed land would 

need an incremental level of control. The rule also states that the pollutant loadings from 

older stormwater management systems shall be reduced as necessary to restore or 

maintain the designated uses of waters. As the proposed numeric nutrients criteria 

interpret the existing narrative criterion, EPA assumes any such reductions requiring 

costs are not a consequence of the proposed criteria. The NRC suggested that existing 

State rules are not being fully complied with and EPA should not consider them to be part 

of the baseline. EPA’s assumption of compliance with the 1982 Stormwater Rule is 

based on FDEP’s economic analysis indicating that post-1982 development would not 

need additional controls. Given the State’s cyclical monitoring schedule, existing ambient 

monitoring data may not yet fully reflect nutrient reductions because the rule has only 

been in effect since July 2009. Other controls that target the quantity of stormwater

runoff from low-density residential land may not be as cost effective as the Urban Turf 

Fertilizer Rule. Thus, EPA did not estimate an incremental level of control to be needed 

for low-density residential land. 
Page 177 of 221

Identifying water as impaired under the proposed rule could result in changes to 

MS4 NPDES permit requirements for urban runoff, so that Florida waters meet the 

proposed criteria. However, the combination of additional pollution controls required will 

likely depend on the specific nutrient reduction targets, the controls already in place, and 

the relative amounts of nitrogen and phosphorus pollution contained in urban runoff at 

each particular location. Because stormwater programs are usually implemented using an 

iterative approach – with the installation of controls followed by monitoring and reevaluation – estimating the complete set of pollution controls required to meet a 

particular water quality target would require detailed site-specific analysis.

Although it is difficult to predict the complete set of potential additional 

stormwater controls that may be required to meet the numeric criteria that supports State 

designated uses in incrementally impaired waters, EPA estimated potential costs for 

additional treatment by assessing the amount of urban land that may require additional 

stormwater controls. FDEP has previously assumed that all urban land developed after 

adoption of Florida's 1982 stormwater rule would be in compliance with the Phase 1 rule 

and EPA believes it is reasonable to make a similar assumption for this proposed rule.224

Using this assumption, EPA used GIS analysis of land use data obtained from the State of 

Florida225 to identify the amount of remaining urban land located near incrementally 

impaired waters. For Phase I MS4s, EPA used a range of acres with 46,700 acres as the 

upper bound and zero acres as the lower bound, because Phase I MS4 urban areas already 

 224 FDEP. 2010. FDEP Review of EPA’s "Preliminary Estimate of Potential Compliance Costs and Benefits 

Associated with EPA’s Proposed Numeric Nutrient Criteria for Florida": Prepared January 2010 by the 

Environmental Protection Agency. Florida Department of Environmental Protection, Division of 

Environmental Assessment and Restoration.

225 Florida Geographic Data Library, 2009. 
Page 178 of 221

must implement controls to the “maximum extent practicable.” As such, these 

municipalities may not need to achieve additional reductions if existing requirements are 

already fully implemented. EPA similarly estimated ranges of acreage needing 

stormwater controls for Phase II MS4 areas, and non-MS4 urban areas. GIS analysis of 

land use data indicates that land in Phase II MS4 and non-MS4 urban areas are low 

density residential. For the urban land that is not low density residential, some additional 

structural BMPs may be necessary to comply with EPA’s numeric nutrient criteria. 

Because nutrient reductions from low density residential land under the existing Urban 

Turf Fertilizer Rule are likely sufficient, and the State of Florida asserts that urban land 

developed after 1982 (77.9% of urban land) would not need additional controls for 

compliance with EPA’s numeric nutrient criteria, EPA estimated that approximately 

27,700 to 43,100 acres of Phase II MS4 urban land and 19,600 to 28,900 acres of urban 

land outside of MS4 areas may require additional stormwater controls to meet EPA’s 

numeric nutrient criteria. The actual acreage may be somewhere within the range. Using 

this procedure, EPA estimated that 47,300 to 118,700 acres may require additional 

stormwater controls.

The cost of stormwater pollution controls can vary widely. FDEP tracks the cost 

of stormwater retrofit projects throughout the State that it has provided grant funding 

for. 226 EPA estimated control costs based on the average unit costs, $19,300, across all 

projects from FDEP (2012c) to account for the mix of project types likely to be installed 

 226 FDEP. 2010. "Appendix 3: Cost Analysis for Municipal Discharge using 30 Year Annualization and 

Florida MS4 Numeric Nutrient Criteria Cost Estimation," In: FDEP Review of EPA’s “Preliminary 

Estimate of Potential Compliance Costs and Benefits Associated with EPA’s Proposed Numeric Nutrient 

Criteria for Florida”: Prepared January 2010 by the Environmental Protection Agency. Florida 

Department of Environmental Protection, Division of Environmental Assessment and Restoration.
Page 179 of 221

based on their current prevalence in grant funding throughout the state. The NRC 

suggested that higher pollutant removals may be obtained by more advanced stormwater 

control measures such as bioretention or other vegetated infiltration, which may be more 

costly than the current set of FDEP-funded projects. NRC (2009) indicates annual peracre costs could range from $300 per acre to $3,500 per acre.227 EPA does not have the 

necessary information to exactly compare this source with EPA’s average unit costs of 

$19,300, but believes EPA’s unit costs are captured within the higher end of the range. 

Given that the costs may be comparable to the NRC suggested projects and the retrofit 

data is specific to projects that Florida has already implemented therefore making them 

more likely to be implemented for future projects, EPA continues to use costs from the 

Florida specific retrofit project data.

EPA multiplied the average capital costs per acre ($19,300) of the FDEP projects 

by the number of acres potentially requiring controls to estimate the potential incremental 

stormwater capital costs associated with the proposed rule. EPA then used FDEP's 

estimate of operation and maintenance (O&M) costs (at 5% of capital costs), and 

annualized capital costs using FDEP's discount rate of 7% over 20 years. This analysis 

indicates that urban runoff control costs could range from approximately $131.9 million 

to $330.9 million. Table VI(C)(2) summarizes these estimates. 

Table VI(C)(1): Estimated Incremental Urban Stormwater Costs

Urban Land Type

Estimated Acres 

Potentially Needing 

Controls1

Capital Costs 

(million $)2

O&M Costs (million 

$/yr)3

Annual Costs 

(million $/yr)4

MS4 Phase I Urban 0 - 46,700 $0 - $901.4 $0 - $45.1 $0.0 - $130.2

MS4 Phase II Urban 27,700 - 43,100 $534.0 - $832.8 $26.7 - $41.6 $77.1 - $120.3

 227 NRC (2009) does not provide the discount rate, useful life, or annual O&M costs it uses to estimate 

annual costs. 
Page 180 of 221

Non-MS4 Urban 19,600 - 28,900 $379.2 - $557.5 $19.0 - $27.9 $54.8 - $80.5

Total 47,300 - 118,700 $913.2 - $2,291.7 $45.7 - $114.6 $131.9 - $330.9

1. Phase I MS4s range represents implementation of BMPs to the MEP resulting in compliance with EPA’s rule or 

controls needed on all pre-1982 developed land that is not low density residential; Phase II MS4s and urban land outside 

of MS4s represent controls needed on all pre-1982 developed land that is not low density residential. Assumes that up to 

46% of land associated with unassessed waters would require controls.

2. Represents acres needing controls multiplied by median unit costs of stormwater retrofit costs from FDEP (2010b).

3. Represents 5% of capital costs.

4. Capital costs annualized at 7% over 20 years plus annual O&M costs.

2. Agricultural Costs 

EPA’s GIS analysis of land use indicates that agriculture accounts for about 

15,312 to 38,140 acres of land near incrementally impaired waters. This differs 

substantially from the Inland Rule where over 800,000 acres of agricultural land use were 

identified in watersheds draining to potentially incrementally impaired WBIDs, because 

agriculture is a much more prevalent land use inland than near the coast. Agricultural 

runoff can be a source of nitrogen and phosphorus to estuaries, coastal waters and south 

Florida inland flowing waters through the application of fertilizer to crops and pastures 

and from animal wastes. For waters impaired by nitrogen and phosphorus pollution, the 

1999 Florida Watershed Restoration Act established that agricultural BMPs should be the 

primary instrument to implement TMDLs. Thus, additional waters identified by the State 

as impaired under the proposed rule may result in State requirements or provisions to 

reduce the discharge of nitrogen and/or phosphorus to incrementally impaired waters 

through the implementation of BMPs. The NRC suggested that for Phase I, the 

incremental agricultural land area identified was likely underestimated. EPA addressed 

this finding by including land area associated with potentially impaired unassessed waters 

in this analysis. 
Page 181 of 221

EPA estimated the potential costs of additional agricultural BMPs by evaluating 

land use data. BMP programs designed for each type of agricultural operation and their 

costs were taken from a study of agricultural BMPs to help meet TMDL targets in the 

Caloosahatchee River, St. Lucie River, and Lake Okeechobee watersheds. Three types of 

BMP programs were identified in this study. The first program, called the “Owner 

Implemented BMP program,” consists of a set of BMPs that land owners might 

implement without additional incentives. The second program, called the “Typical BMP 

program,” is the set of BMPs that land owners might implement under a reasonably 

funded cost share program or a modest BMP strategy approach. The third program, called 

the “Alternative BMP program,” is a more expensive program designed to supplement 

the “Owner Implemented BMP program” and “Typical BMP program” if additional 

reductions are necessary.

The BMPs in the “Owner Implemented BMP Program” and “Typical BMP 

Program” are similar to the BMPs verified as effective by FDEP and adopted by FDACS. 

EPA did not find BMPs in the “Alternative BMP Program” similar to the BMPs in the 

FDACS BMP manual, despite the NRC suggestion that the “Alternative BMP Program” 

would be needed to meet NNC. EPA has also found no indication that the “Alternative 

BMP Program,” which includes edge-of-farm stormwater chemical treatment, has been 

implemented through TMDLs to meet water quality standards for nutrients in watersheds 

with significant contributions from agriculture (e.g., Lake Okeechobee). EPA also found 

that TMDLs cite the Florida Department of Agriculture and Consumer Services’ 

(FDACS) BMP manual as a source of approved BMPs. Therefore, for purposes of this 

analysis, EPA believes it is reasonable to assume that nutrient controls for agricultural 
Page 182 of 221

sources are best represented by the combination of the “Owner Implemented BMP 

Program” and “Typical BMP Program” and not the more stringent “Alternative BMP 

Program” controls. This assumption corroborates EPA’s intent for the nutrient criteria to 

provide the same level of protection as Florida’s narrative criteria.

Table VI(C)(2) summarizes the potential incremental costs of BMPs on 

agricultural lands in the watersheds of incrementally impaired estuaries, coastal waters 

and south Florida inland flowing waters for each agricultural category. This analysis 

indicates that incremental agricultural costs resulting from the proposed numeric nutrient 

criteria may be estimated at $0.3 - $0.7 million per year.

Table VI(C)(2). Potential Incremental Agricultural BMP Costs 

Agricultural Category Area 

Potentially 

Needing 

Controls 

(acres)a

“Owner Implemented 

BMP Program” plus 

”Typical BMP 

Program” Unit Costs 

(2010$/ac/yr)b

Total “Owner 

Implemented BMP 

Program” and 

”Typical BMP 

Program” Costs 

(2010$/yr)

Animal Feeding 20 - 39 $18.56 $400 - $700

Citrus 0 $156.80 $0

Fruit Orchardsc 0 - 7 $156.80 $0 - $1,100

Cow Calf Production, 

Improved Pastures 1,115 - 4,568 $15.84 $17,700 - $72,400

Cow Calf Production, 

Rangeland and 

Wooded Pasture

1,145 - 1,995 $4.22 $4,800 - $8,400

Cow Calf Production, 

Unimproved Pastures 299 - 1,346 $4.22 $1,300 - $5,700

Cropland and Pasture 

Land (general)d

10,195 -

18,467 $27.26 $277,900 - $503,300

Dairies 0 $334.40 $0

Field Crop (Hayland) 

Production 479 - 1,397 $18.56 $8,900 - $25,900

Horse Farms 34 - 123 $15.84 $500 - $1,900

Ornamental Nursery 4 - 8 $70.00 $300 - $600

Floriculturee 0 $70.00 $0

Row Crop 228 - 246 $70.40 $16,100 - $17,300

Sod/Turf Grass 0 $35.20 $0

Other Areasf 565 - 1,069 $18.56 $10,500 - $19,800

Totalg 14,085 -

29,265 -- $338,300 - $657,200
Page 183 of 221

Table VI(C)(2). Potential Incremental Agricultural BMP Costs 

Agricultural Category Area 

Potentially 

Needing 

Controls 

(acres)a

“Owner Implemented 

BMP Program” plus 

”Typical BMP 

Program” Unit Costs 

(2010$/ac/yr)b

Total “Owner 

Implemented BMP 

Program” and 

”Typical BMP 

Program” Costs 

(2010$/yr)

Note: Detail may not add to total due to independent rounding.

a. Low end of range represents acres associated with impaired assessed waters assuming none of the 

unassessed waters would be impaired under the proposed rule; high end of range represent low end 

plus controls on the watersheds associated with impaired unassessed waters (estimated based on 

proportional impairment to assessed waters) for which EPA has not already identified a need for 

controls for baseline or impaired assessed waters. Based on GIS analysis of land use data from five 

water management districts (for entire State)

b. Cost estimates from SWET (2008); representative of 2010 prices (personal communication with D. 

Bottcher, 2010).

c. Owner/typical BMP unit costs based on costs for citrus crops.

d. Owner/typical BMP unit costs based on average costs for improved pastures, unimproved/wooded 

pasture, row crops, and field crops.

e. Owner/typical BMP unit costs based on costs for ornamental nurseries.

f. Includes FLUCCS Level 3 codes 2230, 2400, 2410, and 2540.

g. Excludes land not in production.

3. Septic System Costs

Some nutrient reductions from septic systems may be necessary for incrementally 

impaired waters to meet the numeric nutrient criteria in this proposed rule. Several 

nutrient-related TMDLs in Florida identify septic systems as a significant source of 

nitrogen and phosphorus pollution. Some of the ways to address pollution from septic 

systems may include greater use of inspection programs and repair of failing systems, 

upgrading existing systems to advanced nutrient removal, installation of decentralized 

cluster systems where responsible management entities would ensure reliable operation 

and maintenance, and connecting households and businesses to wastewater treatment 

plants. Because of the cost, time, and issues associated with new wastewater treatment 

plant construction, EPA assumed that the most likely strategy to reduce nutrient loads 

from septic systems would be to upgrade existing conventional septic systems to 

advanced nutrient removal systems.
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Septic systems in close proximity to surface waters are more likely to contribute 

nutrient loads to waters than distant septic systems. Florida Administrative Code provides 

that in most cases septic systems should be at least 75 feet from surface waters (F.A.C. 

64e-6.005(3)). In addition, many of Florida’s existing nutrient-related TMDLs identify 

nearby failing septic systems as contributing to nutrient impairments in surface waters. 

For this economic analysis, EPA assumed that some septic systems located near 

incrementally impaired waters may be required to upgrade to advance nutrient removal 

systems. However, the distance that septic systems can be safely located relative to these 

surface waters depends on a variety of site-specific factors. Because of this uncertainty, 

EPA assumed that septic systems located within 500 feet of any water (based on land use 

types) in watersheds containing or, in the case of coastal waters, surrounding 

incrementally impaired estuaries, coastal waters or south Florida inland flowing waters 

may need to be upgraded from conventional to advanced nutrient removal systems. The 

NRC agreed with the 500-ft threshold, but found that the exclusion of septic systems in 

springsheds is a deficiency of EPA’s analysis. This proposed rule does not include 

criteria for springsheds.

EPA used GIS analysis of data obtained from the Florida Department of Health 

228 that provides the location of active septic systems in the State to identify the 

potentially affected septic systems. This analysis yielded 5,952 to 10,784 active septic 

systems that may be affected by the proposed rule.

 228 FDOH. 2010. Bureau of Onsite Sewage GIS Data Files. Florida Department of Health, Division of 

Environmental Health. <http://www.doh.state.fl.us/Environment/programs/EhGis/EhGisDownload.htm>.
Page 185 of 221

EPA evaluated the cost of upgrading existing septic systems to advanced nutrient 

removal systems. The NRC also recommended that EPA consider permeable reactive 

barriers (PRB) in their technology costs and take into account any additional Floridaspecific costs related to septic system upgrades (e.g., performance-based treatment 

systems, under Florida regulations, need to be designed by Florida licensed professional 

engineers). EPA included this technology in the cost analysis, resulting in the range of 

upgrade capital costs from $3,300 to $8,800 per system. See the Economic Analysis for 

further detail. For O&M costs, EPA relied on a study that compared the annual costs 

associated with various septic system treatment technologies including conventional 

onsite sewage treatment and disposal system and fixed film activated sludge systems. 

Based on this study, EPA estimated the incremental O&M costs for an advanced system 

to be $650 per year.229 In addition, homeowners would also incur a biennial permit fee of 

$100 (or $50 per year) for the upgraded system. Thus, based on annual O&M costs of 

$700 and annualizing capital costs at 7% over 20 years, total annual costs could range 

from approximately $1,000 to $1,500 for each upgrade. EPA estimated the total annual 

costs of upgrading septic systems by multiplying this range of unit costs with the number 

of systems identified for upgrade. Using this method, total annual costs for upgrading 

septic systems in incrementally impaired watersheds could range from $6.0 million to 

$16.2 million.

 229 Chang, N., M. Wanielista, A. Daranpob, F. Hossain, Z. Xuan, J. Miao, S. Liu, Z. Marimon, and S. 

Debusk. 2010. Onsite Sewage Treatment and Disposal Systems Evaluation for Nutrient Removal. FDEP 

Project #WM 928. Report Submitted to Florida Department of Environmental Protection, by Stormwater 

Management Academy, Civil, Environmental, and Construction Engineering Department, University of 

Central Florida.
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D. Governmental Costs

The proposed rule may result in the identification of incrementally impaired 

waters that would require the development of additional TMDLs. As the principal State 

regulatory agency implementing water quality standard, FDEP may incur costs associated 

with developing additional TMDLs. EPA’s analysis identified 95 (based on the analysis 

of assessed waters) to 183 (including potentially impaired unassessed waters) 

incrementally impaired waters (WBIDs). 

Because current TMDLs for estuaries and coastal waters in Florida include an 

average of approximately four WBIDs each, EPA estimates that the State of Florida may 

need to develop and adopt approximately 24 to 46 additional TMDLs. The NRC 

recommended applying Florida-specific TMDL development costs from a FDEP report 

detailing FDEP TMDL program costs. EPA used a range of costs from a 2001 EPA 

study that found the cost of developing a TMDL at different levels of aggregation and the 

Florida-specific TMDL cost estimates are within this range of costs.230,231 For this 

analysis, EPA used the estimates for a single cause of impairment and adjusted the costs 

to account for the possibility that a TMDL may need to address more than one pollutant 

(because most of the incrementally impaired waters in EPA's analysis exceeded the 

criteria for more than one pollutant). Under this assumption, EPA estimated the average 

TMDL cost to be approximately $47,000 ($28,000 on average for one pollutant, plus 

$6,000 on average for the other pollutant and adjusted to 2010 dollars). EPA also 

 230 USEPA. 2001. The National Costs of the Total Maximum Daily Load Program (Draft Report). EPA841-D-01-003. U.S. Environmental Protection Agency, Office of Water, Washington DC. 231 EPA did not adjust these estimates to account for potential reductions in resources required to develop 

TMDLs given that scientifically based numeric targets were developed as part of this proposed rule. Costs 

for these TMDLs are thus likely to be an overestimate.
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estimated unit costs based on the high end of typical TMDL development costs, plus an 

additional $6,000 for the second nutrient. Escalating to 2010 dollars, the high range of 

TMDL development cost of $212,000. For 24 to 46 TMDLs, total costs for incremental 

TMDL development could be $1.1 million to $10.2 million.

FDEP currently operates its TMDL schedule on a five-phase cycle that rotates 

through Florida’s five basins over five years. Under this schedule, completion of TMDLs 

for high priority waters will take 9 years; it will take an additional 5 years to complete the 

process for medium priority waters. Assuming all the incremental impairments are high 

priority and FDEP develops the new TMDLs over a 9-year period, annual costs could be 

$0.1 to $1.1 million.

Should the State of Florida submit current TMDL targets as Federal site specific 

alternative criteria (SSAC) for EPA review and approval, EPA believes it is reasonable to 

assume that information used in the development of the TMDLs will substantially reduce 

the time and effort needed to provide a scientifically defensible justification for such 

applications. If EPA’s assumption is incorrect and there were to be increased costs for the 

SSAC process, EPA expects that such cost underestimation would be cancelled out by 

continuing to include the costs of developing the scientifically based numeric targets for 

new TMDLs. Thus, EPA did not separately analyze any incremental costs associated 

with SSAC.

Similarly, state and local agencies regularly monitor TN and TP in ambient 

waters. These data are the basis for the extensive IWR database maintained by the State 

of Florida. Because Florida is currently monitoring TN, TP, and chlorophyll-a
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concentrations in many waters, EPA assumed that the rule is unlikely to have a 

significant impact on costs related to water quality monitoring activities.

E. DPVs

EPA is proposing several options for DPVs. For this analysis, EPA assumed that 

the DPVs equal the numeric nutrient criteria for the segment to which the stream 

discharges. If the State of Florida were to choose any of the other three proposed options 

for DPVs, then these costs may be over- or underestimated. To estimate whether the 

DPVs are being met, EPA used the same minimum data requirements (e.g., four data 

points in one year with at least one data point each in summer and winter seasons) and 

attainment criteria (no more than one exceedance in a three-year period) for evaluating 

the criteria. EPA used data from estuary pour points from any station within 500 feet of 

and within the same WBID as the pour point. For south Florida pour points EPA did not 

use the data from the technical report, but used all data from the WBID in which the pour 

point is located to assess impairment.

For this analysis, EPA assumed that any WBID containing a pour point exceeding 

the criteria would be designated as impaired. EPA then identified the watersheds that 

contain or surround, in the case of coastal waters, those incrementally impaired WBIDs. 

See Appendix G of the economic analysis for more information.

Table VI(E). Summary of Potential Incremental Costs Associated with DPVs

Source Category Total Potential Incremental Annual Cost ($/year)

Municipal Wastewater $29.4 - $29.6

Industrial Dischargers $0.0

Urban Stormwater $9.5 - $185.1

Agriculture $0.5 - $0.9

Septic Systems $2.0 - $3.0

Government/Program Implementation1 $0.0 - $0.1

Total $41.4 - $218.6
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1. Assuming 3 TMDLs for 13 WBIDs (approximately 4 WBIDs per TMDL) over a 9-year period.

F. Summary of Costs

Table VI(F) summarizes EPA's estimates of potential incremental costs associated 

with additional State and private sector activities to meet the numeric criteria supporting 

State designated uses. Note, these total costs include costs associated with unassessed 

waters. Because of uncertainties in the pollution controls ultimately implemented by the 

State of Florida, actual costs may vary depending on the site-specific source reductions

needed to meet the new numeric criteria. 

Table VI(F). Summary of Potential Annual Costs 1 (2010 dollars)

Sector Annual Cost (millions)2

Municipal Wastewater $44.1 - $49.7

Industrial Dischargers $15.2

Urban Stormwater $131.9 - $330.9

Agriculture $0.3 - $0.7

Septic Systems $6.0 - $16.2

Government/Program Implementation (TMDLs) $0.1 - $1.1

Downstream Protection Values $41.4 - $218.6

Total $239.0 - $632.4

1. Includes costs for assessed, unassessed, and DPVs.

2. Low end of range represents estimated costs under the assumption that none of the unassessed waters 

would be impaired under the proposed rule; high end of range represents costs associated with the assumption 

of proportional impairment of unassessed waters.

EPA also calculated the potential costs to Florida households. Given the uncertainty 

regarding the magnitude of the estimated costs ultimately borne by households, EPA 

sought to minimize that uncertainty with a selective though matched set of potential costs 

and potentially affected households. Although GIS analysis could be used to overlay 

maps of affected populations and facilities with incrementally impaired watersheds, a 

simpler more direct approach is to assume that all households in Florida are either served 

by a wastewater treatment plant or septic system, and pay taxes that would support 
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implementation programs conducted by the State. In addition, because the sector with 

the largest costs is urban stormwater, EPA decided to include this sector as well. Thus,

EPA decided to look at the total costs of the two rules across all households in Florida. 

Also, given the cost-pass-through of agriculture costs and industrial costs to consumers 

outside the State of Florida, EPA did not consider them for the estimate of average costs 

per households in Florida. Therefore, EPA also calculated the total costs for municipal 

wastewater and stormwater controls, septic upgrades, and government/program 

implementation costs for both the proposed rule and the Inland rule and compared this 

sum to the total number of households in the State. This may underestimate actual 

household costs if some costs are not borne equally by households statewide, but instead 

are concentrated within the watersheds for which controls are needed. EPA’s total 

estimated annual cost for compliance with this proposed rule, and the Inland rule, 

represents $44 to $108 per household per year for both rules across all households in 

Florida. This equals $0.123.60 to $0.309 cents per daymonth per household in Florida. 

Please refer to Section 13 in the Economic Analysis for more information.

EPA also considered whether the potential costs of this proposed rule could result 

in employment impacts. Environmental regulations can both increase and decrease 

employment, and whether the net effect is positive or negative depends on many factors. 

See Chapter 13 of the Economic Analysis for further discussion.

G. Benefits

Since elevated concentrations of nutrients in surface waters can result in adverse 

ecological effects, human health impacts, and negative economic impacts, EPA expects 

Comment [E46]: OMB edit to express costs as 

per month instead of per day.
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the proposed numeric nutrient criteria to result in significant ecological, human health, 

and economic benefits to Florida. For example, excess nutrients in water can cause 

eutrophication, which can lead to harmful (sometimes toxic) algal blooms, loss of rooted 

plants, and decreased dissolved oxygen. In turn, these results can lead to adverse impacts 

on aquatic life, fishing, swimming, wildlife watching, camping, and drinking water. 

Excess nutrients can also cause: nuisance surface scum, reduced food for herbivorous 

wildlife, fish kills, alterations in fish communities, and unsightly shorelines that can 

decrease property values. Excessive nutrient loads can also lead to harmful algal blooms 

(HABs), which can cause a range of adverse human health effects including dermal, 

gastrointestinal, neurological, and respiratory problems, and in severe cases, may even 

result in fatalities.

Nutrient impairment is currently a major concern for many bays, estuaries, and 

coasts within the United States, and is particularly severe for many Florida waters. 

FDEP’s 2010 report identifies approximately 569 square miles (364,160 acres) of 

estuaries (about 23 percent of assessed estuarine area) and 102 square miles (65,280 

acres) of coastal waters (about 1.5 percent of assessed coastal waters) as impaired by 

nutrients. These impairments may have a significant impact on the value of 

environmental goods and services provided by the affected waterbodies. For example, the 

losses of submerged aquatic vegetation resulting from eutrophication can have significant

economic impacts. In 2009, Florida seagrass communities supported an estimated harvest 

of $23 million for just six species of commercial fish and shellfish.232

 232 Crist, C. 2010. Seagrass Awareness Month. Proclamation by the Governor Charlie Crist of the State of 

Florida. Florida Department of Environmental Protection.

Comment [E47]: OMB edit accepted.
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In Florida’s environment and economy, the tourism-focused goods and services 

provided by its bays, estuaries, and coastal waters are particularly valuable. The tourism 

industry of Florida’s nearshore counties contributes approximately $12.4 billion (2004 

dollars) to the State’s economy annually.233 Coral reefs are especially important 

contributors to Florida’s tourism sector. Reef-related recreational expenditures on 

activities such as snorkeling, scuba diving, fishing, and glass bottom boating in four 

counties in southeastern Florida for a one year period in 2000-2001 totaled $5.4 

billion.234

The proposed rule will help reduce nitrogen and phosphorus concentrations in 

Florida’s estuaries, coastal waters and south Florida inland flowing waters. In turn, this 

reduction will improve ecological function and prevent further degradation that can result 

in substantial economic benefits to Florida citizens. EPA's economic analysis document 

describes in detail many of the potential benefits associated with meeting the numeric 

criteria in the proposed rule for nitrogen and phosphorus, including reduced human health 

risks, ecological benefits and functions, improved recreational opportunities, aesthetic 

enhancements and others. 

1. Monetized Benefits Estimates

Reducing nutrient concentrations will increase services provided by water 

resources to recreational users. For example, some coastal waters that are not usable for 

 233 NOEP. 2006. Coastal Economy Data. National Ocean Economics Program. 

<www.oceaneconomics.org/Market/coastal/coastalEcon.asp>. 234 Johns, G.M., V.R. Leeworthy, F.W. Bell, and M.A. Bonn. 2001. Socioeconomic Study of Reefs in 

SoutheastFlorida. Final Report prepared by Hazen and Sawyer, Hollywood, FL, for Broward County, Palm 

Beach County, Miami-Dade County, Monroe County, Florida Fish and Wildlife Conservation Commission, 

and National Oceanic and Atmospheric Administration.
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recreation may become available following implementation of the rule, thereby 

expanding recreation options for residential users and tourists. Other waters that are 

available for recreation can become more attractive for users by making recreational trips 

more enjoyable. Individuals may also take trips more frequently if they enjoy their 

recreational activities more. In addition to recreational improvements, the proposed rule 

is expected to generate nonuse benefits from bequest, altruism, and existence 

motivations. Individuals may value the knowledge that water quality is being maintained, 

ecosystems are being protected, and populations of individual species are healthy, 

independently from any use value. 

EPA used a benefits transfer function based on meta-analysis of surface water 

valuation studies to estimate both use and nonuse benefits from improvements in surface 

water. This approach is based on the method used to quantify nonmarket benefits in the 

2009 Environmental Impact and Benefits Assessment for Final Effluent Guidelines and 

Standards for the Construction and Development Category (EPA, 2009), also used in the 

economic analysis of the Inland Rule. The approach quantifies benefits based on reachspecific baseline water quality and the estimated change in pollutant concentrations. The 

approach translates reductions in nutrients into an indicator of overall water quality (via a 

“water quality ladder,” or WQL) and values these improvements in terms of household 

willingness to pay (WTP) for the types of uses (e.g., as fishing and swimming) that are 

supported by different water quality levels. 

EPA calculated the baseline WQL scores for incrementally affected waters by 

comparing the water quality observations to criteria. For coastal waters, only Chl-a

criteria are applicable, and for these waters, EPA estimated baseline WQL scores based 
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on Chl-a exceedances only. For other marine waters, EPA developed estimates of 

baseline water quality based on comparing the water quality observations to the 

applicable criteria in the following order: 1) exceedances of proposed TN criteria; 2) 

exceedances of proposed TP criteria; and 3) exceedances of proposed Chl-a criteria. The 

baseline WQL score is based on the percent exceedance of the applicable criterion value. 

EPA assumes all incrementally impaired waters will meet the proposed criteria and 

estimated the potential changes for each waterbody. EPA estimated that up to 163 

unassessed WBIDs may be incrementally impaired, but water quality data for these 

waters are not available. To estimate the potential benefits associated with these 

potentially impaired unassessed waters, EPA estimated the same percent exceedance of 

the potentially impaired assessed waters. Because EPA’s estimates of monetized benefits 

only reflect the water quality improvements for WBIDs, and not HUC-12s, these 

potential benefits are underestimated and should not be directly compared to costs, which 

include HUC-12 costs. EPA then estimated monetized benefit values of these water 

quality improvements using benefits transfer based on a meta-regression of 45 studies 

that value water quality improvements in surface waters. Using the meta-analysis EPA 

estimated a household WTP function with independent variables that characterize 1) the 

underlying study and methodology used, 2) demographic and other characteristics of the 

surveyed populations, 3) geographic region and scale, and 4) resource characteristics and 

improvements. More details on the meta-analysis can be found in the Economic Analysis.

Using this function, EPA derived household WTP estimates for both full time and 

part time residents of the State. EPA estimated that seasonal residents live in the State for 

approximately four months of the year; therefore EPA weighted household WTP values 
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for seasonal residents by one third. EPA then weighted household WTP estimates by the 

percentage of State water miles that are expected to improve. EPA estimated total 

benefits by multiplying the weighted household WTP value with the total number of 

benefiting households. EPA estimated the number of full time residents by dividing the 

total State population by average household size for the State as provided by the U.S. 

Census Bureau’s 2010 American Community Survey (U.S. Census Bureau, 2010). The 

number of part-time households in Florida is based on Smith and House (2006), who 

used survey data to estimate the number, timing, and duration of temporary moves to 

Florida at peak seasons. EPA used the Smith and House (2006) results and U.S. Census 

Bureau (2010) statistics on household size to estimate the number of part-time 

households in Florida. Total monetized benefits, including monetized benefits of 

unassessed waters, may be in the range from $39.0 million to $53.4 million annually, as 

shown in Table VI(F). The range reflects EPA’s assumptions regarding the location of 

unassessed waters that might be incrementally impaired. 

Because EPA’s estimates of monetized benefits only reflect use and nonuse 

values associated with water quality improvements to Florida residents (full and part 

time), these potential benefits are likely underestimated compared to costs. The 

population considered in the benefits analysis of the rule does not include households 

outside of Florida that may also hold values for water resources in the State of Florida. 

Even if per household values for out-of-State residents are small, they may be significant 

in the aggregate if these values are held by a substantial number of out-of-State 

households. EPA notes that four times as many out-of-State and foreign tourists visit the 

State’s saltwater beaches each year as State residents do. Not including out-of-State 
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residents in the analysis is likely to result in an underestimation of the total benefits of 

improved water quality. Although these monetized benefits estimates do not account for 

all potential economic benefits arising from the proposed rule, they help to demonstrate 

the economic importance of restoring and protecting Florida waters from the impacts of 

nitrogen and phosphorus pollution. 

Table VI(F): Potential Annual State Benefits Associated with the Proposed Criteria 

Including Unassessed Waters (2010 dollars)

WTP Estimate Average Benefit per Mile1 Total Benefits (millions)2

Lower 5% Bound $8,200 $17.2 - $23.6

Mean $18,500 $39.0 - $53.4

Upper 95% Bound $34,500 $72.5 - $99.4

1. Total benefits divided by 2,102 incrementally impaired assessed miles.

2. Benefits per mile times the number of incrementally impaired miles; based on between 2,102 

and 2,882 potentially improved miles. The low end of the range represents assessed waters 

only, and the high end of the range includes unassessed waters.

VII. Statutory and Executive Order Reviews 

A. Executive Orders 12866 (Regulatory Planning and Review) and 13563 (Improving 

Regulation and Regulatory Review) 

Under Executive Order 12866 (58 FR 51735, October 4, 1993), this action is a 

"significant regulatory action.” Accordingly, EPA submitted this action to the Office of 

Management and Budget (OMB) for review under Executive Orders 12866 and 13563 

(76 FR 3821, January 21, 2011) and any changes made in response to OMB 

recommendations have been documented in the docket for this action. This proposed rule 

does not establish any requirements directly applicable to regulated entities or other 

sources of nitrogen and phosphorus pollution. Moreover, existing narrative water quality 

criteria in State law already require that nutrients not be present in waters in 
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concentrations that cause an imbalance in natural populations of flora and fauna in 

estuaries and coastal waters in Florida and in south Florida inland flowing waters.

B. Paperwork Reduction Act

This action does not impose any direct new information collection burden under 

the provisions of the Paperwork Reduction Act, 44 U.S.C. 3501 et seq. Actions to 

implement these standards may entail additional paperwork burden. Burden is defined at 

5 CFR 1320.3(b). This action does not include any information collection, reporting, or 

record-keeping requirements.

C. Regulatory Flexibility Act 

The Regulatory Flexibility Act (RFA) generally requires an agency to prepare a 

regulatory flexibility analysis of any rule subject to notice and comment rulemaking 

requirements under the Administrative Procedure Act or any other statute unless the 

agency certifies that the rule will not have significant economic impact on a substantial 

number of small entities. Small entities include small businesses, small organizations, and 

small governmental jurisdictions.

For purposes of assessing the impacts of this action on small entities, small 

entity is defined as: (1) A small business as defined by the Small Business

Administration's (SBA) regulations at 13 CFR 121.201; (2) a small governmental 

jurisdiction that is a government of a city, county, town, school district or special district 

with a population of less than 50,000; and (3) a small organization that is any not-forprofit enterprise that is independently owned and operated and is not dominant in its 

field.

Comment [E48]: OMB edit accepted.

Comment [E49]: OMB edit accepted.
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Under the CWA water quality standards program, states must adopt water 

quality standards for their waters and must submit those water quality standards to EPA 

for review and approval or disapproval; if the Agency disapproves a state standard and 

the state does not adopt appropriate revisions to address EPA’s disapproval, EPA must 

promulgate standards consistent with the statutory and regulatory requirements. EPA also 

has the authority to promulgate water quality standards in any case where the 

Administrator determines that a new or revised standard is necessary to meet the 

requirements of the CWA. State standards approved by EPA (or EPA-promulgated 

standards) are implemented through various water quality control programs including the 

NPDES program, which limits discharges to navigable waters except in compliance with 

an NPDES permit. The CWA requires that all NPDES permits include any limits on 

discharges that are necessary to meet applicable water quality standards.

Thus, under the CWA, EPA’s promulgation of water quality standards

establishes standards that the State of Florida implements through the NPDES permit 

process. The State has discretion in developing discharge limits, as needed to meet the 

standards. This proposed rule does not itself establish any requirements that are 

applicable to small entities. As a result of this action, the State of Florida will need to 

ensure that permits it issues include any limitations on discharges necessary to comply 

with the standards established in the final rule. In doing so, the State will have a number 

of choices associated with permit writing (e.g., relating to compliance schedules, 

variances, etc.). While Florida’s implementation of the rule may ultimately result in new 

or revised permit conditions for some dischargers, including small entities, EPA’s action, 

by itself, does not impose any of these requirements on small entities; that is, these 
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requirements are not self-implementing. Thus, I certify that this rule will not have a 

significant economic impact on a substantial number of small entities.

D. Unfunded Mandates Reform Act

Title II of the Unfunded Mandates Reform Act of 1995 (UMRA), Public Law 

104-4, establishes requirements for Federal agencies to assess the effects of their 

regulatory actions on state, local, and tribal governments and the private sector. Under 

section 202 of the UMRA, EPA generally must prepare a written statement, including a 

cost-benefit analysis, for proposed and final rules that include a ”Federal mandate” that 

may result in expenditures to state, local, and Tribal governments, in the aggregate, or to 

the private sector, of $100 million or more in any one year. A “Federal mandate,” is any 

provision in federal statute or regulation that would impose an enforceable duty on State, 

local or Tribal governments or the private sector.235 Before promulgating an EPA rule for 

which a written statement is needed under section 202, section 205 of the UMRA 

generally requires EPA to identify and consider a reasonable number of regulatory 

alternatives and adopt the least costly, most cost-effective or least burdensome alternative 

that achieves the objectives of the rule. The provisions of section 205(a) do not apply 

when they are inconsistent with law. Moreover, section 205(b) allows EPA to adopt an 

alternative other than the least costly, most cost-effective or least burdensome alternative 

if the Administrator publishes with the final rule an explanation of why that alternative 

was not adopted. Before EPA establishes any regulatory requirements that may 

significantly or uniquely affect small governments, including Tribal governments, it must 

 235 A “Federal mandate” does not include conditions of Federal assistance and generally does not include 

duties arising from participation in a voluntary Federal program.
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have developed under section 203 of the UMRA a small government agency plan. The 

plan must provide for notifying potentially affected small governments, enabling officials 

of affected small governments to have meaningful and timely input in the development of 

EPA regulatory proposals with significant Federal intergovernmental mandates, and 

informing, educating, and advising small governments on compliance with the regulatory 

requirements.

This proposed rule contains no Federal mandates (under the regulatory 

provisions of Title II of the UMRA) for state, local, or Tribal governments or the private 

sector. As these water quality criteria are not self-implementing, EPA’s proposed rule 

does not regulate or affect any entity. Because this proposed rule does not regulate or 

affect any entity, it therefore is not subject to the requirements of sections 202 and 205 of 

UMRA.

EPA determined that this proposed rule contains no regulatory requirements 

that might significantly or uniquely affect small governments. Moreover, water quality 

standards, including those promulgated here, apply broadly to dischargers and are not 

uniquely applicable to small governments. Thus, this proposed rule is not subject to the 

requirements of section 203 of UMRA.

E. Executive Order 13132 (Federalism)

This action does not have federalism implications. It will not have substantial 

direct effects on the States, on the relationship between the national government and the 

States, or on the distribution of power and responsibilities among the various levels of 

government, as specified in Executive Order 13132. EPA’s authority and responsibility to 
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promulgate Federal water quality standards when state standards do not meet the

requirements of the CWA is well established and has been used on various occasions in 

the past. The proposed rule would not substantially affect the relationship between EPA 

and the States and Territories, or the distribution of power or responsibilities between 

EPA and the various levels of government. The proposed rule would not alter Florida’s 

considerable discretion in implementing these water quality standards. Further, this

proposed rule would not preclude Florida from adopting water quality standards that EPA 

concludes meet the requirements of the CWA, either before or after promulgation of the 

final rule, which would eliminate the need for Federal standards. Thus, Executive Order 

13132 does not apply to this proposed rule.

Although section 6 of Executive Order 13132 does not apply to this action, EPA 

communicated with the State of Florida to discuss the Federal rulemaking process. In the 

spirit of Executive Order 13132, and consistent with EPA policy to promote 

communications between EPA and State and local governments, EPA specifically solicits 

comment on this proposed rule from State and local officials.

F. Executive Order 13175 (Consultation and Coordination with Indian Tribal 

Governments)

Subject to the Executive Order 13175 (65 FR 67249, November 9, 2000) EPA 

may not issue a regulation that has tribal implications, that imposes substantial direct 

compliance costs, and that is not required by statute, unless the Federal government 

provides the funds necessary to pay the direct compliance costs incurred by Tribal 

governments, or EPA consults with tribal officials early in the process of developing the 
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proposed regulation and develops a tribal summary impact statement. EPA has concluded 

that this action may have tribal implications. However, the rule will neither impose 

substantial direct compliance costs on tribal governments, nor preempt Tribal law. 

In the State of Florida, there are two Indian tribes, the Seminole Tribe of Florida 

and the Miccosukee Tribe of Indians of Florida, with flowing waters. Both tribes have

been approved for treatment in the same manner as a state (TAS) status for CWA 

sections 303 and 401 and have federally-approved water quality standards in their 

respective jurisdictions. These tribes are not subject to this proposed rule. However, this 

rule may impact the tribes because the numeric criteria for Florida will apply to waters 

adjacent to the tribal waters.

EPA consulted with Tribal officials early in the process of developing this 

regulation to permit them to have meaningful and timely input into its development. At a 

consultation teleconference held on March 1, 2012, EPA summarized the available 

information regarding this proposed rule, and requested comments on the proposal and its 

possible effects on tribal waters. Information relevant to this proposed action and the 

related Tribal consultation is posted on the EPA Tribal Portal site at 

http://www.epa.gov/tribal/consultation/index.htm. EPA specifically solicits additional 

comment on this proposed rule from tribal officials.

G. Executive Order 13045 (Protection of Children From Environmental Health and 

Safety Risks)

This action is not subject to EO 13045 (62 FR 19885, April 23, 1997) because it is 

not economically significant as defined in EO 12866, and because the Agency believes 
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that this rule will result in the reduction of environmental health and safety risks that 

could present a disproportionate risk to children.

H. Executive Order 13211 (Actions That Significantly Affect Energy Supply, Distribution, 

or Use)

This rule is not a “significant energy action” as defined in Executive Order 13211,

“Actions Concerning Regulations That Significantly Affect Energy Supply,

Distribution, or Use” (66 FR 28355 (May 22, 2001)), because it is not likely to have a 

significant adverse effect on the supply, distribution, or use of energy.

I. National Technology Transfer Advancement Act of 1995

Section 12(d) of the National Technology Transfer and Advancement Act of 1995 

(“NTTAA”), Public Law 104–113, section 12(d) (15 U.S.C. 272 note) directs EPA to use 

voluntary consensus standards in its regulatory activities unless to do so would be 

inconsistent with applicable law or otherwise impractical. Voluntary consensus standards 

are technical standards (e.g., materials specifications, test methods, sampling procedures, 

and business practices) that are developed or adopted by voluntary consensus standards 

bodies. The NTTAA directs EPA to provide Congress, through OMB, explanations when 

the Agency decides not to use available and applicable voluntary consensus standards.

This proposed rulemaking does not involve technical standards. Therefore, EPA is 

not considering the use of any voluntary consensus standards.

J. Executive Order 12898 (Federal Actions To Address Environmental Justice in 

Minority Populations and Low-Income Populations)
Page 204 of 221

Executive Order (EO) 12898 (Feb. 16, 1994) establishes Federal executive policy 

on environmental justice. Its main provision directs Federal agencies, to the greatest 

extent practicable and permitted by law, to make environmental justice part of their 

mission by identifying and addressing, as appropriate, disproportionately high and 

adverse human health or environmental effects of their programs, policies, and activities 

on minority populations and low-income populations in the United States.

EPA has determined that this proposed rule does not have disproportionately high 

and adverse human health or environmental effects on minority or low-income 

populations because it would afford a greater level of protection to both human health 

and the environment if these numeric nutrient criteria are promulgated for Class I, Class 

II and Class III waters in the State of Florida.
Page 205 of 221

Water Quality Standards for the State of Florida’s Estuaries, Coastal Waters, and 

South Florida Inland Flowing Waters; Proposed Rule Page 204 of 220

List of Subjects in 40 CFR Part 131

Environmental protection, Water quality standards, Nitrogen and phosphorus pollution,

Nutrients, Florida.

Dated: November 30, 2012.

Lisa P. Jackson,

Administrator.

For the reasons set out in the preamble, EPA proposes to amend 40 CFR Part 131 as 

follows:

PART 131 – WATER QUALITY STANDARDS 

1. The authority citation for Part 131 continues to read as follows:

Authority: 33 U.S.C. 1251 et seq.

Subpart D-[Amended]

2. Section 131.45 is added to read as follows:

§ 131.45 Water Quality Standards for the State of Florida’s Estuaries, Coastal 

Waters, and South Florida Inland Flowing Waters

(a) Scope. This section promulgates numeric criteria for nitrogen and phosphorus 

pollution for Class I, Class II, and Class III waters in the State of Florida. This section 

also contains provisions for site-specific alternative criteria.
Page 206 of 221

(b) Definitions. — (1) Canal means a trench, the bottom of which is normally 

covered by water with the upper edges of its two sides normally above water.

(2) Coastal water means all marine waters that have been classified as Class II 

(Shellfish Propagation or Harvesting) or Class III (Recreation, Propagation and 

Maintenance of a Healthy, Well-Balanced Population of Fish and Wildlife) water bodies 

pursuant to Section 62-302.400, F.A.C., extending to three nautical miles from shore that 

are not classified as estuaries.

(3) Estuary means predominantly marine regions of interaction between rivers

and nearshore ocean waters, where tidal action and river flow mix fresh and salt water. 

Such areas include bays, mouths of rivers, and lagoons that have been classified as Class 

II (Shellfish Propagation or Harvesting) or Class III (Recreation, Propagation and 

Maintenance of a Healthy, Well-Balanced Population of Fish and Wildlife) water bodies 

pursuant to Section 62-302.400, F.A.C., excluding wetlands.

(4) Everglades Agricultural Area (EAA) means those lands described in Florida 

Statute Section 373.4592 (1994) subsection (15).

(5) Everglades Protection Area (EvPA) means Water Conservation Areas 1

(which includes the Arthur R. Marshall Loxahatchee National Wildlife Refuge), 2A, 2B, 

3A, and 3B, and the Everglades National Park.

(6) Inland flowing waters means inland predominantly fresh surface water streams

that have been classified as Class I (Potable Water Supplies) or Class III (Recreation, 

Propagation and Maintenance of a Healthy, Well-Balanced Population of Fish and 

Wildlife) water bodies pursuant to Section 62–302.400, F.A.C., excluding wetlands (e.g.,

sloughs).
Page 207 of 221

(7) Marine Lake means a slow-moving or standing body of marine water that 

occupies an inland basin that is not a stream, spring, or wetland.

(8) Predominantly fresh waters means surface waters in which the chloride 

concentration at the surface is less than 1,500 milligrams per liter.

(9) Predominantly marine waters means surface waters in which the chloride 

concentration at the surface is greater than or equal to 1,500 milligrams per liter.

(10) South Florida inland flowing waters means inland flowing waters in the 

South Florida Nutrient Watershed Region, which encompasses the waters south of Lake 

Okeechobee, the Caloosahatchee River (including Estero Bay) watershed, and the St. 

Lucie watershed.

(11) State means the State of Florida, whose transactions with the U.S. EPA in 

matters related to 40 CFR 131.45 are administered by the Secretary, or officials delegated 

such responsibility, of the Florida Department of Environmental Protection (FDEP), or 

successor agencies.

(12) Stream means a free-flowing, predominantly fresh surface water in a defined 

channel, and includes rivers, creeks, branches, canals, freshwater sloughs, and other 

similar water bodies. 

(13) Surface water means water upon the surface of the earth, whether contained 

in bounds created naturally or artificially or diffused. Water from natural springs shall be 

classified as surface water when it exits from the spring onto the Earth's surface.

(14) Tidal creek means a relatively small coastal tributary with variable salinity that 

lies at the transition zone between terrestrial uplands and the open estuary.

(c) Criteria for Florida Waters.
Page 208 of 221

(1) Criteria for Estuaries.

The applicable total nitrogen (TN), total phosphorus (TP), and chlorophyll a 

criteria for estuaries are shown in Table 1.

 

Table 1. EPA’s Numeric Criteria for Florida’s Estuaries (in geographic order 

Northwest to Northeast)

Proposed Criteria

Perdido Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Upper Perdido Bay 0101 0.59 0.042 5.2

Big Lagoon 0102 0.26 0.019 4.9

Central Perdido Bay 0103 0.47 0.031 5.8

Lower Perdido Bay 0104 0.34 0.023 5.8

Pensacola Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Blackwater Bay 0201 0.53 0.022 3.9

Upper Escambia 

Bay 0202 0.43 0.025 3.7

East Bay 0203 0.50 0.021 4.2

Santa Rosa Sound 0204 0.34 0.018 4.1

Lower Escambia 

Bay 0205 0.44 0.023 4.0

Upper Pensacola 

Bay 0206 0.40 0.021 3.9

Lower Pensacola 

Bay 0207 0.34 0.020 3.6

Santa Rosa Sound 0208 0.33 0.020 3.9

Santa Rosa Sound 0209 0.36 0.020 4.9

Choctawhatchee 

Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Eastern 

Choctawhatchee 

Bay

0301 0.47 0.025 8.1

Central 

Choctawhatchee 

Bay

0302 0.36 0.019 3.8

Western 

Choctawhatchee 

Bay

0303 0.21 0.012 2.4
Page 209 of 221

St. Andrews 

Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

East Bay 0401 0.31 0.014 4.6

St. Andrews Sound 0402 0.14 0.009 2.3

Eastern St. Andrews 

Bay 0403 0.24 0.021 3.9

Western St. 

Andrews Bay 0404 0.19 0.016 3.1

Southern St. 

Andrews Bay 0405 0.15 0.013 2.6

North Bay 1 0406 0.22 0.012 3.7

North Bay 2 0407 0.22 0.014 3.7

North Bay 3 0408 0.21 0.016 3.4

West Bay 0409 0.23 0.022 3.8

St. Joseph Bay SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

St. Joseph Bay 0501 0.25 0.018 3.8

Apalachicola 

Bay

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

St. George Sound 0601 0.53 0.019 3.6

Apalachicola Bay 0602 0.51 0.019 2.7

East Bay 0603 0.76 0.034 1.7

St. Vincent Sound 0605 0.52 0.016 11.9

Apalachicola

Offshore 0606 0.30 0.008 2.3

Alligator 

Harbor

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Alligator Harbor 0701 0.36 0.011 2.8

Alligator Offshore 0702 0.33 0.009 3.1

Alligator Offshore 0703 0.33 0.009 2.9

Ochlockonee

Bay+

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Ochlockonee-St. 

Marks Offshore 0825 0.79 0.033 2.7

Ochlockonee

Offshore 0829 0.47 0.019 1.9

Ochlockonee Bay 0830 0.66 0.037 1.8

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

St. Marks River 

Offshore 0827 0.51 0.022 1.7

St. Marks River 0828 0.55 0.030 1.2
Page 210 of 221

Big Bend/ 

Apalachee Bay+

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Econfina Offshore 0824 0.59 0.028 4.6

Econfina 0832 0.55 0.032 4.4

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Fenholloway 0822 1.15 0.444 1.9

Fenholloway

Offshore 0823 0.48 0.034 10.3

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

SteinhatcheeFenholloway 

Offshore 

0821 0.40 0.023 4.1

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Steinhatchee River 0819 0.67 0.077 1.0

Steinhatchee 

Offshore 0820 0.34 0.018 3.5

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Steinhatchee 

Offshore 0818 0.39 0.032 4.8

Suwannee 

River+

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Suwannee Offshore 0817 0.78 0.049 5.2

Springs Coast+

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Waccasassa River 

Offshore 0814 0.38 0.019 3.9

Cedar Keys 0815 0.32 0.019 4.1

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Crystal River 0812 0.35 0.013 1.3

Crystal-Homosassa 

Offshore 0813 0.36 0.013 2.1

Homosassa River 0833 0.47 0.032 1.9

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(ug/L)

Chassahowitzka 

River 0810 0.32 0.010 0.7
Page 211 of 221

Chassahowitzka 

River Offshore 0811 0.29 0.009 1.7

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Weeki Wachee 

River 0808 0.32 0.010 1.6

Weeki Wachee 

Offshore 0809 0.30 0.009 2.1

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Pithlachascotee 

River 0806 0.50 0.022 2.4

Pithlachascotee

Offshore 0807 0.32 0.011 2.5

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Anclote River 0804 0.48 0.037 4.7

Anclote Offshore 0805 0.31 0.011 3.2

Anclote Offshore 

South 0803 0.29 0.008 2.6

Lake Worth 

Lagoon/

Loxahatchee

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

North Lake Worth 

Lagoon 1201 0.55 0.067 4.7

Central Lake Worth 

Lagoon 1202 0.57 0.089 5.3

South Lake Worth 

Lagoon 1203 0.48 0.034 3.6

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Lower Loxahatchee 1301 0.68 0.028 2.7

Middle Loxahatchee 1302 0.98 0.044 3.9

Upper Loxahatchee 1303 1.25 0.072 3.6

St. Lucie

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Lower St. Lucie 1401 0.58 0.045 5.3

Middle St. Lucie 1402 0.90 0.120 8.4

Upper St. Lucie 1403 1.22 0.197 8.9

Indian River 

Lagoon SEGMENT SEGMENT ID TN*(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)
Page 212 of 221

Mosquito Lagoon 1501 1.18 0.078 7.5

Banana River 1502 1.17 0.036 5.7

Upper Indian River 

Lagoon 1503 1.63 0.074 9.2

Upper Central 

Indian River Lagoon 1504 1.33 0.076 9.2

Lower Central 

Indian River Lagoon 1505 1.12 0.117 8.7

Lower Indian River 

Lagoon 1506 0.49 0.037 4.0

Halifax River

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Upper Halifax River 1601 0.75 0.243 9.4

Lower Halifax River 1602 0.63 0.167 9.6

Guana, 

Tolomato, 

Matanzas, 

Pellicer

SEGMENT SEGMENT ID TN*

(mg/L)

TP*

(mg/L)

Chl-a*1

(μg/L)

Upper GTMP 1701 0.77 0.144 9.5

Lower GTMP 1702 0.53 0.108 6.1

Lower St. Johns 

River

SEGMENT SEGMENT ID TN*

(mg/L) TP* (mg/L) Chl-a*1

(μg/L)

Lower St. Johns River 1801 0.75 0.095 2.5

Trout River 1802 1.09 0.108 3.6

Trout River 1803 1.15 0.074 7.7

Nassau River

SEGMENT SEGMENT ID TN*

(mg/L) TP* (mg/L) Chl-a*1

(μg/L)

Lower Nassau 1901 0.33 0.113 3.2

Middle Nassau 1902 0.40 0.120 2.4

Upper Nassau 1903 0.75 0.125 3.4

St. Marys River

SEGMENT SEGMENT ID TN*

(mg/L) TP* (mg/L) Chl-a*1(μg/L)

Lower St. Marys River 2002 0.27 0.045 3.0

Middle St. Marys 

River 2003 0.44 0.036 2.7

1 Chlorophyll a is defined as corrected chlorophyll, or the concentration of chlorophyll a remaining after 

the chlorophyll degradation product, phaeophytin a, has been subtracted from the uncorrected chlorophyll a

measurement.

* For a given water body, the annual geometric mean of TN, TP, or chlorophyll a, concentrations shall not 

exceed the applicable criterion concentration more than once in a three-year period. + In these four areas (collectively referred to as the “Big Bend region”), coastal and estuarine waters are 

combined. Criteria for the Big Bend region apply to the coastal and estuarine waters in that region. 
Page 213 of 221

(2) Criteria for Tidal Creeks.

The applicable total nitrogen (TN), total phosphorus (TP), and chlorophyll a 

criteria for predominantly marine tidal creeks are shown in §131.45(c)(1), Table 1. The 

applicable TN and TP criteria for predominantly freshwater tidal creeks are shown in 

Table 2.

Table 2. EPA’s Numeric Criteria for Florida’s Predominantly Freshwater Tidal 

Creeks

Nutrient Watershed Region

Instream Protection Value Criteria

TN (mg/L) * TP (mg/L) *

Panhandle West a 0.67 0.06

Panhandle East b 1.03 0.18

North Central c 1.87 0.30

West Central d 1.65 0.49

Peninsula e 1.54 0.12

Watersheds pertaining to each Nutrient Watershed Region (NWR) were based principally on the NOAA 

coastal, estuarine, and fluvial drainage areas with modifications to the NOAA drainage areas in the West 

Central and Peninsula Regions that account for unique watershed geologies. For more detailed information 

on regionalization and which WBIDs pertain to each NWR, see the Technical Support Document.

a Panhandle West region includes: Perdido Bay Watershed, Pensacola Bay Watershed, Choctawhatchee 

Bay Watershed, St. Andrews Bay Watershed, Apalachicola Bay Watershed. b Panhandle East region includes: Apalachee Bay Watershed, and Econfina/Steinhatchee Coastal Drainage 

Area.

c North Central region includes the Suwannee River Watershed.

d

West Central region includes: Peace, Myakka, Hillsborough, Alafia, Manatee, Little Manatee River 

Watersheds, and small, direct Tampa Bay tributary watersheds south of the Hillsborough River Watershed. 

e Peninsula region includes: Waccasassa Coastal Drainage Area, Withlacoochee Coastal Drainage Area, 

Crystal/Pithlachascotee Coastal Drainage Area, small, direct Tampa Bay tributary watersheds west of the 

Hillsborough River Watershed, Sarasota Bay Watershed, small, direct Charlotte Harbor tributary 

watersheds south of the Peace River Watershed, Caloosahatchee River Watershed, Estero Bay Watershed, 

Kissimmee River/Lake Okeechobee Drainage Area, Loxahatchee/St. Lucie Watershed, Indian River 

Watershed, Daytona/St. Augustine Coastal Drainage Area, St. Johns River Watershed, Nassau Coastal 

Drainage Area, and St. Marys River Watershed. * For a given water body, the annual geometric mean of TN or TP concentrations shall not exceed the 

applicable criterion concentration more than once in a three-year period.

(3) Criteria for Marine Lakes.
Page 214 of 221

The applicable total nitrogen (TN), total phosphorus (TP) and chlorophyll a

criteria for marine lakes are shown in Table 3.

Table 3. EPA’s Numeric Criteria for Florida’s Marine Lakes

Long Term Average Lake 

Colora and Alkalinity

EPA Final 

Chl-ab,*

μg/L

EPA Final TN and TP Criteria

[Range]

TN

mg/L

TP

mg/L

Colored lakesc 20 1.27

[1.27-2.23]

0.05

[0.05-0.16]

Clear lakes, high 

alkalinityd

20 1.05

[1.05-1.91]

0.03

[0.03-0.09]

Clear lakes, low 

alkalinitye

6 0.51

[0.51-0.93]

0.01

[0.01-0.03] a Platinum-cobalt units (PCU) assessed as true color free from turbidity b Chl-a is defined as corrected chlorophyll, or the concentration of chl-a remaining

after the chlorophyll degradation product, phaeophytin a, has been subtracted from the uncorrected

chl-a measurement. c Long-term color > 40 PCU and alkalinity > 20 mg/L CaCO3 d Long-term color ≤ 40 PCU and alkalinity > 20 mg/L CaCO3 e Long-term color ≤ 40 PCU and alkalinity ≤ 20 mg/L CaCO3

* For a water body, the annual geometric mean of chl-a, TN or TP concentrations shall

not exceed the applicable criterion concentration more than once in a three-year period.

(4) Criteria for Coastal Waters.

The applicable chlorophyll a criteria for coastal waters are shown in Table 4.

Table 4. EPA’s Numeric Criteria for Florida’s Coastal Waters

Coastal Region Coastal Segment+ Approximate Location ChlorophyllRS-a1

* (mg/m3)

Panhandle

1 Alabama border 2.41

2 Pensacola Bay Pass 2.57

3 1.44

4 1.16

5 1.06

6 1.04

7 1.14

8 Choctawhatchee Bay Pass 1.23

9 1.08
Page 215 of 221

10 1.09

11 1.11

12 1.18

13 1.45

14 St. Andrews Bay Pass 1.74

15 St. Joseph Bay Pass 2.75

16 2.39

17 Southeast St. Joseph Bay 3.47

West Florida 

Shelf

18 3.96

19 Tampa Bay Pass 4.45

20 3.37

21 3.25

22 2.95

23 2.79

24 2.98

25 3.24

26 Charlotte Harbor 4.55

27 4.22

28 3.67

29 4.16

30 5.70

31 4.54

324.03

33 Fort Myers 4.61

Atlantic Coast

34 Biscayne Bay 0.92

35 0.26

36 0.26

37 0.24

38 0.21

39 0.21

40 0.20

41 0.20

42 0.21

43 0.25

44 0.57

45 St. Lucie Inlet 1.08

46 1.42

47 1.77

48 1.55

49 1.44

50 1.53

51 1.31

52 1.40

53 1.80

54 Canaveral Bight 2.73

55 2.33

56 2.28

57 2.06

58 1.92

59 1.76

60 1.72
Page 216 of 221

61 2.04

62 1.92

63 1.86

64 1.95

65 2.41

66 2.76

67 2.80

68 3.45

69 Nassau Sound 3.69

70 3.78

71 Georgia border 4.22 1 ChlorophyllRS-a is remotely sensed calculation of chlorophyll a concentrations. 

* For a given water body, the annual geometric mean of the chlorophyll a concentration shall not exceed 

the applicable criterion concentration more than once in a three-year period. + Please see TSD for location of Coastal Segments (Volume 2: Coastal Waters, Section 1.3).

(5) Criteria for South Florida Inland Flowing Waters.

The applicable criteria for south Florida inland flowing waters that flow into 

downstream estuaries include the downstream protection value (DPV) for total nitrogen

(TN) and total phosphorus (TP) derived pursuant to the provisions of §131.45(c)(6).

These criteria are not applicable to waters within the lands of the Miccosukee and 

Seminole Tribes, the Everglades Protection Area (EvPA), or the Everglades Agricultural 

Area (EAA).

(6) Criteria for Protection of Downstream Estuaries and South Florida marine 

waters. (i) A downstream protection value (DPV) for stream tributaries that flow into a 

downstream estuary or south Florida marine water (i.e., downstream water) is the 

allowable concentration of total nitrogen (TN) and/or total phosphorus (TP) applied at the 

point of entry into the downstream water. The applicable DPV for any stream flowing 

into a downstream water shall be determined pursuant to paragraphs (c)(6)(ii), (iii), (iv),

or (v) of this section. The methods available to derive DPVs should be considered in the 

order listed. Contributions from stream tributaries upstream of the point of entry location 

must result in attainment of the DPV at the point of entry into the downstream water. If 
Page 217 of 221

the DPV is not attained at the point of entry into the downstream water, then the 

collective set of streams in the upstream watershed does not attain the DPV, which is an 

applicable water quality criterion for the water segments in the upstream watershed. The 

State or EPA may establish additional DPVs at upstream tributary locations that are 

consistent with attaining the DPV at the point of entry into the downstream water. The 

State or EPA also have discretion to establish DPVs to account for a larger watershed 

area (i.e., include waters beyond the point of reaching water bodies that are not streams as 

defined by this rule).

(ii) In instances where available data and/or resources provide for use of a 

scientifically defensible and protective system-specific application of water quality 

simulation models with results that protect the designated uses and meet all applicable

numeric nutrient criteria for the downstream water, the State or EPA may derive the DPV 

for TN and TP from use of a system-specific application of water quality simulation 

models. The State or EPA may designate the wasteload and/or load allocations from a 

TMDL established or approved by EPA as DPV(s) if the allocations from the TMDL will 

protect the downstream water's designated uses and meet all applicable numeric nutrient

criteria for the downstream water.

(iii) When the State or EPA has not derived a DPV for a stream pursuant to 

paragraph (c)(6)(ii) of this section, and where a reference condition approach is used to 

derive the downstream water’s TN, TP and chlorophyll a criteria, then the State or EPA 

may derive the DPV for TN and TP using a reference condition approach based on TN 

and TP concentrations from the stream pour point, coincident in time with the data record 

from which the downstream receiving water segment TN and TP criteria were developed, 
Page 218 of 221

and using the same data screens and reference condition approach as were applied to the 

downstream water’s data. 

(iv) When the State or EPA has not derived a DPV pursuant to paragraph 

(c)(6)(ii) or (c)(6)(iii) of this section, then the State or EPA may derive the DPV for TN 

and TP using dilution models based on the relationship between salinity and nutrient 

concentrations.

(v) When the State or EPA has not derived a DPV pursuant to paragraph 

(c)(6)(ii), (c)(6)(iii), or (c)(6)(iv) of this section, then the DPV for TN and TP is the 

applicable TN and TP criteria for the receiving segment of the downstream water as 

described in §131.45(c)(1), or as described in Section 62-302.532(a)-(h), F.A.C. for 

downstream waters where EPA-approved State criteria apply.

(vi) The State and EPA shall maintain a record of DPVs they derive based on the 

methods described in paragraphs (c)(6)(ii), (iii), (iv), and (v) of this section, as well as a 

record supporting their derivation, and make such records available to the public. The 

State and EPA shall notify one another and provide a supporting record within 30 days of 

derivation of DPVs pursuant to paragraphs (c)(6)(i), (ii), (iii), (iv), or (v) of this section.

DPVs derived pursuant to these paragraphs do not require EPA approval under Clean 

Water Act §303(c) to take effect.

(d) Applicability. (1) The criteria in paragraphs (c)(1) through (6) of this section 

apply to certain Class I, Class II, and Class III waters in Florida, and apply concurrently 

with other applicable water quality criteria, except when:

(i) State water quality standards contain criteria that are more stringent for a 

particular parameter and use;
Page 219 of 221

(ii) The Regional Administrator determines that site-specific alternative criteria 

apply pursuant to the procedures in paragraph (e) of this section; or

(iii) The State adopts and EPA approves a water quality standards variance to the 

Class I, Class II, or Class III designated use pursuant to §131.13 that meets the applicable 

provisions of State law and the applicable Federal regulations at §131.10.

(2) The criteria established in this section are subject to the State's general rules of 

applicability in the same way and to the same extent as are the other Federally-adopted 

and State-adopted numeric criteria when applied to the same use classifications.

(e) Site-specific Alternative Criteria.

(1) The Regional Administrator may determine that site-specific alternative

criteria shall apply to specific surface waters in lieu of the criteria established in 

paragraph (c) of this section. Any such determination shall be made consistent with 

§131.11.

(2) To receive consideration from the Regional Administrator for a determination 

of site-specific alternative criteria, an entity shall submit a request that includes proposed 

alternative numeric criteria and supporting rationale suitable to meet the needs for a 

technical support document pursuant to paragraph (e)(3) of this section. The entity shall 

provide the State a copy of all materials submitted to EPA, at the time of submittal to 

EPA, to facilitate the State providing comments to EPA. Site-specific alternative criteria 

may be based on one or more of the following approaches.

(i) Replicate the process for developing the estuary criteria in paragraph (c)(1) of 

this section. 
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(ii) Replicate the process for developing the tidal creek criteria in paragraph (c)(2) 

of this section.

(iii) Replicate the process for developing the marine lake criteria in paragraph 

(c)(3) of this section.

(iv) Replicate the process for developing the coastal criteria in paragraph (c)(4) of 

this section.

(v) Replicate the process for developing the south Florida inland flowing water 

criteria in paragraph (c)(5) of this section.

(vi) Conduct a biological, chemical, and physical assessment of water body 

conditions. 

(vii) Use another scientifically defensible approach protective of the designated 

use.

(3) For any determination made under paragraph (e)(1) of this section, the 

Regional Administrator shall, prior to making such a determination, provide for public 

notice and comment on a proposed determination. For any such proposed determination, 

the Regional Administrator shall prepare and make available to the public a technical 

support document addressing the specific surface waters affected and the justification for 

each proposed determination. This document shall be made available to the public no 

later than the date of public notice issuance.

(4) The Regional Administrator shall maintain and make available to the public an 

updated list of determinations made pursuant to paragraph (e)(1) of this section as well as 

the technical support documents for each determination.
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(5) Nothing in this paragraph (e) shall limit the Administrator's authority to 

modify the criteria in paragraph (c) of this section through rulemaking.

(f) Effective date. This section is effective [date 60 days after publication of final 

rule].