Attachment J - 

Rationale for Conformed STA NPDES and EFA Permits 
1

Rationale for Conformed STA NPDES and EFA Permits 

I. General Rationale 

All portions of STA NPDES and EFA permits not cited below were conformed to eliminate all 

references to the non-conforming elements of the Long-Term Plan, the EFAA’s moderating 

provisions, and/or any extended compliance schedule past December 31, 2006, as required by the 

2010 Order. They were also conformed to incorporate the WQBEL specified in this Amended 

Determination. The following rationale is provided for changed provisions that do not clearly 

fall in the above categories for: 1) all or most of the permits; and 2) specific permits. Provisions 

were also changed to make the permits consistent with the CWA and the implementing NPDES 

regulations. All added language is denoted by red. 

II. Changed Provisions in All or Most Permits 

1. The above named permittee is hereby authorized to construct and operate the facilities 

required by this permit shown on the application and other documents attached hereto or on file 

with the Department and made a part hereof and specifically described as follows:

 This or similar language is found on the cover page of several permits. Because the 

 application and other documents refer to projects specified in the Long-Term Plan that 

 are now deemed as non-conforming, USEPA deleted reference to them. 

2. Replacing “stormwater” with “non-process wastewater” or “wastewater” 

 This is most often found in the first pages of each permit where the type of wastewater 

 that is treated by each STA is described. USEPA’s view is that the wastewater treated by 

 the STAs is not solely stormwater or return flows from agriculture. It may also include 

 groundwater, stormwater, and other water sources or wastewater types. Due to the varied 

 nature of that wastewater, it is not appropriate to specify it as “stormwater”. 

3. WQBEL language - All EFF TP monitoring results for this parameter shall be reported as separate weekly 

values without rounding to whole numbers. The results shall also be reported as FWM annual averages that are 

calculated based on the FWM of the weekly values. The results shall also be reported as GM annual averages that 

are calculated based on all sample point weekly values collected when discharge occurs in the previous 12 months. 

All FWM and GM annual averages shall be reported to the nearest whole number (i.e., 10.5 ppb shall be reported as 

11 ppb; 10.49 ppb shall be reported as 10 ppb). All SWU TP monitoring results shall be reported as separate weekly 

values without rounding to whole numbers. All results shall also be reported as monthly averages and as FWM 

annual averages. The monthly averages and FWM annual averages shall be calculated based on the FWM of the 

weekly values and shall be reported to the nearest whole number (i.e., 10.5 ppb shall be reported as 11 ppb; 10.49 

ppb shall be reported as 10 ppb). 

 This added language or its equivalent is found as footnotes in either Part I.A.1 of each 

 NPDES permit or below the table ‘Discharge Limitations and Associated Monitoring 

 Requirements’ near the end of each EFA permit. Authority for these reporting 

 requirements is provided by CWA Section 308(a) and 40 CFR Parts 122.41(j), 

 122.48(a), and 122.43(a). It is important that the separate weekly phosphorus data be 

 reported without rounding so that it can be assessed as appropriate in the future. Because 
2

 the TP water quality criterion, the various components of the four-part test, and the two 

 WQBEL components are all expressed as whole numbers, compliance with the WQBEL 

 should also be assessed using whole numbers. The rounding requirements specified are 

 consistent with historical USEPA practice and interpretation. The calculation of GM 

 annual averages is consistent with the derivation of the WQBEL. 

Beginning at the end of April after the permit effective date and at the end of each April 

thereafter, the permittee shall report the FWM annual average using data it collected for the prior 

12 months. Beginning at the end of April after the permit effective date and at the end of each 

April thereafter, the permittee shall report the GM annual average using data it collected for each 

of the prior 3 years.

 This language was added to either Part I.A.5 of the STA NPDES permits or as a footnote 

 near the end of each EFA permit below the table ‘Discharge Limitations and Associated 

 Monitoring Requirements’. 

4. No violations for the annual average limit will be deemed to have occurred until data have 

been compiled for the first 12 months after the issuance date of the permit. The “annual 

average” effluent limitation is a rolling average equal to the flow-weighted arithmetic mean of 

the effluent samples collected during consecutive reporting periods which comprise one year.

For parameters that are measured at least once per month, the annual average shall be computed 

at the end of each month and is equal to the arithmetic mean of the monthly average of that 

month and of each of the previous eleven months. No violations for the annual average limit will 

be deemed to have occurred until data have been compiled for the first 12 months after the 

issuance date of the permit. For the first 11 months after issuance of this permit, the monitoring 

results for this parameter shall be recorded on the DMR as MNR. Starting with the 12th month 

and lasting until the expiration of this permit, the monitoring results for this parameter shall be 

recorded on the DMR as a 12-month moving flow-weighted average.

 This language was in a footnote in either Part I.A.1 of each NPDES permit or below the 

 EFA permit table ‘Discharge Limitations and Associated Monitoring 

 Requirements’. Based on this language, permit TP monitoring results were required to be 

 reported as a moving annual average and where a limit applied, compliance was assessed 

 monthly. As discussed in the Amended Determination WQBEL summary and attached 

 TSD, the underlying TP water quality criterion is a long-term (decades) value. 

 Although TP is known to vary spatially and temporally above 10 ppb, no imbalance of 

 flora or fauna is observed when the long-term 10 ppb value is maintained. Also, the 

 components of the four part test and the two components of the WQBEL are expressed 

 on an annual timeframe, not on a more frequent basis. For these reasons, it is not 

 necessary to assess permit compliance as a rolling annual average on a monthly basis. 

5. In the year following any two consecutive years where the TP GM annual average exceeds 10 ppb, the permittee 

shall report quarterly the GM of all monthly TP values for that year. If that mean exceeds 10 ppb, the permittee 

shall provide a report to both FDEP and USEPA by the fifteenth of the month following the quarterly report of its 

evaluation of why that mean is as high as it is and the specific steps it is taking to ensure that the TP GM for that 

year will not exceed 10 ppb.
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For the TP FWM WQBEL, the permittee shall report quarterly the average of all monthly FWMs for that year. If 

that average exceeds 18 ppb, the permittee shall provide a report to both FDEP and USEPA by the fifteenth of the 

month following the quarterly report of its evaluation of why that average is as high as it is and the specific steps it 

is taking to ensure that the TP FWM annual average for that year will not exceed 18 ppb.

 This language was added as either Part I.A.6 of each NPDES permit or as a footnote

 below the EFA permit table ‘Discharge Limitations and Associated Monitoring 

 Requirements’ under the authority of CWA Section 308(a) and 40 CFR Part 122.41(j). 

 Because the WQBEL components are expressed as annual averages and compliance is 

 typically assessed at the end of each May-April period, USEPA believes that it is 

 important that the permittee provide early warning of possible WQBEL non-

 compliance and the steps that are being taken to prevent that from occurring. 

6. If the facility does not meet the FWM WQBEL in any year, the permittee shall report the 

annual load of TP discharged by the STA into the Everglades that is in excess of the WQBEL 

load (based on 18 ppb). If the facility does not meet the GM WQBEL in any year, the permittee 

shall separately report the annual load of TP discharged by the STA into the Everglades that is in 

excess of the WQBEL load (based on 10 ppb) for that year and the previous two years.

 This language was added as either Part I.A.7 of each NPDES permit or as a footnote

 below the EFA permit table ‘Discharge Limitations and Associated Monitoring 

 Requirements’ under the authority of CWA Section 308(a) and 40 CFR Part 122.41(j). 

 In order to better evaluate the cumulative impacts and effects of phosphorus intrusion in 

 the Everglades if either WQBEL component is exceeded, calculating the actual excess TP 

 load that occurred will provide useful information. 

7. Samples taken in accordance with Section I.A.1 and submitted monthly as part of the Discharge Monitoring 

Report (DMR) shall be analyzed to provide an annual assessment in the Annual Report as to whether the 

facility is operating within or outside the operational envelope. The assessment shall be based on annual 

inflow volumes and phosphorus loads and shall compare flows and loads to the corresponding average values 

contained in the operational envelope described in Exhibit A (Goforth et al, 2007). If the annual inflow 

volumes or phosphorus loads exceed the corresponding average values of the operational envelope during an 

annual compliance period, the District shall conduct a review of potential causes and include this review in the 

annual report. Departmental concurrence shall be obtained prior to initiating Lake Okeechobee regulatory or 

water supply releases that would result in an exceedance of the maximum levels of flow or phosphorus load 

contained in the operational envelope. 

 This language was added to the NPDES permits for STA-1E, STA-1W, and STA 3/4 to 

 make it consistent with the other NPDES and EFA permits. Assessment of whether the 

 facility is within or outside the operational envelope is useful in determining if the 

 WQBEL is expected to be met and can lead to advanced actions to prevent non-

 compliance with the WQBEL. 

8. The permittee shall submit an Annual Report demonstrating compliance with the conditions of 

this permit and according to the schedule in Section VI. The Annual Report shall provide details 

regarding the status of implementation of the requirements of this permit. Specifically, the report 

will include details regarding: i.) For each downstream transect station, a compilation of the 

water quality, sediment, and vegetation monitoring data collected, as appropriate, and an 
4

assessment of whether the cumulative impact remained unchanged, improved, or worsened from 

the previous year/monitoring.

 This language is in Part I.E of the NPDES permits for STA-1E, STA-1W, and STA 2, as 

 well as Specific Condition 26 of the STA-1E/1W EFA permit and Specific Condition 27 

 of the STA 2 EFA permit. To better evaluate the cumulative impacts and effects of 

 phosphorus intrusion in the Everglades while the Amended Determination remedies are 

 being implemented or if either WQBEL component is exceeded, the above reporting 

 requirement was added to the Annual Report and is based on CWA Section 308(a). 

9. The District shall notify the Department within 24 hours of any unanticipated bypasses of flow 

through the Diversion Structures. The District shall notify the Department as soon as practicable 

in advance of anticipated bypasses, with the exception of routine maintenance. The submitted 

notification shall include a description of the circumstances related to the bypass and a projection 

of the anticipated duration of the bypass. All bypasses occurring through any Structure shall be 

monitored for the parameters listed in the table below. As soon as practicable after cessation of 

all bypasses, the District shall submit a summary of the data collected from the table below and 

identify the duration of the bypasses. Bypasses shall be limited to the shortest time possible and 

are not allowed solely to achieve the WQBEL. Bypasses are subject to and must meet the 

requirements of Items VIII.20, 21, and 22 of this permit [or F.A.C. Sections 62-620.610(20), 

(21), and (22)]. 

Parameter Units Sample Type Frequency

Total Phosphorus mg/l Grab Weekly

Flow CFS Calculated Daily Average

 Part I.E of the NPDES permits and Specific Condition 22 of the STA -1E/1W EFA 

 permit, Specific Condition 25 of the STA 2 EFA permit, Specific Condition 28 of the 

 STA 3/4 EFA permit, and Specific Condition 26 of the STA 5/6 EFA permit were 

 changed to reflect the above language. To make the permits consistent with state and 

 federal permitting regulations, all references to “diversion” were changed to “bypass”. 

 The NPDES regulations at 40 CFR Part 122.41(m) allow some circumstances where 

 water may be bypassed around STAs. In such events, it is important to measure and 

 quantify the flow and TP loading that is bypassed and its duration. That information 

 will help better evaluate cumulative impacts on and effects of phosphorus intrusion in the 

 Everglades, as well as quantify nutrient loadings to the coasts. 

 

10. The laboratory reported PQL for the specific parameter is less than or equal to the permit 

limit or the applicable water quality criteria, if any, stated in Chapter 62-302, F.A.C. Parameters 

that are listed as “report only” in the permit shall use methods that provide a PQL, which is equal 

to or less than the applicable water quality criteria stated in 62-302 FAC; 

 This language is found in Section I.E.1.b of each STA NPDES permit. Because there is 

 now an applicable numeric TP water quality criterion, the phrase “if any” was deleted. 

11. The permittee shall report with the monthly DMR if operation of facilities is impacted by or 

constrained due to requirements under the Endangered Species Act or Migratory Bird Treaty 
5

Act. The report should include the species involved, an estimate of the number of individuals 

involved, actions taken to avoid deleterious impacts on the endangered species, the affect those 

actions had on compliance with any condition of this permit, and an estimate of when facility 

operation will no longer be impacted or constrained.

 This language was added as the last requirement in Section I.E of each NPDES permit 

 and as Specific Condition 26.F in the STA-1E/1W EFA permit, Specific Condition 27.F 

 in the STA 2 EFA permit, Specific Condition 30.F in the STA 3/4 EFA permit, and 

 Specific Condition 28.F in the STA 5/6 EFA permit. The District has already 

 implemented an Avian Protection Program to minimize impacts to black-necked stilts 

 and burrowing owls that nest in the STAs. Historically, the District has delayed STA 

 construction or changed STA operation to protect these species as required by the 

 Endangered Species Act or the Migratory Bird Treaty Act. In recognition that future 

 STA construction or operation may also be affected, the above reporting requirement was 

 added. This provision is added under the authority of 40 CFR Part 122.49. 

12. An Operations Plan shall be developed and submitted by the permittee to the Department no 

later than three months after issuance of the permit. Upon completion of and compliance with 

the requirements specified herein, the permittee shall submit to the Department an updated 

Operations Plan. Until the updated Operations Plan is submitted by the permittee and approved 

by the Department, the previously existing Operations Plan shall remain in effect.

 This language is found in Section VI of the NPDES permits and Specific Condition 8 of 

 the STA-1E/1W EFA permit, Specific Condition 11 of the STA 2 EFA permit, and 

 Specific Condition 10 of the STA 3/4 and 5/6 EFA permits. The Operations Plan 

 describes how the permittee controls STA wastewater treatment and the movement of 

 water within and between STAs. Once compliance with the WQBEL and 

 implementation of the remedies prescribed in this Amended Determination are achieved, 

 these Plans will need to be updated. 

13. The Annual Report shall be received by the Department no later than March 1 of each year 

following the conformance date of this permit. Each Annual Report shall present the 

information for the previous water year, from May 1 to April 30. Upon approval by the 

Department, the District may modify the Annual Report submission date to coincide with 

multiple reporting requirements and time periods needed for data acquisition and analysis.

 This language is found in Part VI of the NPDES permits and Specific Condition 26 of the 

 STA-1E/1W EFA permit, Specific Condition 27 of the STA 2 EFA permit, Specific 

 Condition 30 of the STA 3/4 permit, and Specific Condition 28 of the STA 5/6 EFA 

 permit. Annual Report requirements have been made consistent between the NPDES and 

 EFA permits. 

14. A revised Pollution Prevention Plan (PPP) shall be prepared and implemented in accordance 

with the following schedule:
6

Action Item Scheduled Completion 

Date

1 Develop and Implement revised Pollution 

Prevention Plan 

As needed upon completion 

of and compliance with the 

requirements of this permit

2. Submittal of revised Pollution Prevention Plan if 

additional enhancements are implemented

Changes that warrant 

modifications to the current 

PPP + 90 days

 This language is found in Section VI of the NPDES permits. Because the STAs are 

 considered industrial wastewater facilities, they are required to have a pollution 

 prevention plan that has been adapted to address the treatment and removal of TP under 

 the authority of CWA Section 304(e). The use of such a Plan is consistent with EPA 

 guidance. Once compliance with the WQBEL and implementation of the remedies 

 prescribed in this Amended Determination are achieved, these Plans will need to be 

 updated. 

15. Transect Monitoring: The permittee shall conduct water quality, soil, and vegetation monitoring as 

specified below at a series of sites located along a transect downstream of the STA-1E discharge site to characterize 

the effects of the STA-1E discharge on adjacent marsh areas of the Refuge. Table 6 below identifies five sampling 

sites located along a transect originating at LOXA-135 sampling site in the rim canal adjacent to the STA-1E 

discharge point and extending to the LOXA-139 sampling site located in an unimpacted portion of the marsh. Upon 

demonstration that an additional sampling site or removal of an existing sampling site is warranted, the permittee 

may request a modification to the monitoring program as appropriate. The Department and USEPA shall review 

and approve such requests on a case by case basis. Any alteration in the monitoring program approved by the 

Department and USEPA shall occur in the form of a modification to this permit.

The monitoring site closest to the discharge point (LOX-135) is located in the rim canal and will be used to evaluate 

changes in water quality occurring between the discharge point and the actual marsh. Of the remaining four marsh 

sites, LOXA-136 and LOXA-137 are located in areas currently identified as impacted (i.e., sediment TP 

concentration greater than 500 mg/kg) with the final two sites located in areas currently identified as unimpacted. All water quality, soil, and vegetation samples will be collected and reported for the parameters and at the frequency

specified in the SFWMD’s January 20, 2010 ‘Project WCA-2A Monitoring Plan for STA-2 and Compartment B 

Build-Out Downstream Monitoring Plan’. Water quality grab samples will be collected at each of the transect 

sampling sites identified in Table 6 below on a monthly basis. In addition, sediment samples will be collected at

each marsh site every three years. The sediment samples will be subdivided into floc (if present) and the upper 10 

cm of sediment with each component being analyzed separately for TP and bulk density. The depth of any floc 

layer will also be recorded. To assure that the samples collected are representative of ambient conditions, all marsh 

sampling will be conducted in accordance with the marsh sampling protocols provided in the SFWMD’s Field 

Sampling Quality Manual as refined in the District’s Monitoring Plan for Everglades Protection Area Water 

Conservation Area 1 (WCA1), Project: EVPA. 

 This language was added as Section VII.F in the NPDES permit for STA-1E and its 

 equivalent was added as Section VII.F in the NPDES permits for STA-1W and STA 2. 

 Specific Conditions 23 and 24 in the STA 1E/1W EFA permit and Specific Condition 32 

 in the STA 2 EFA permit were also modified to include equivalent language. The 

 downstream monitoring information is needed to better evaluate the cumulative impacts 

 and effects of phosphorus intrusion in the Everglades while the Amended Determination 

 remedies are being implemented or if either WQBEL component is exceeded. The above 
7

 reporting requirements that periodically assesses water quality, vegetation, and 

 sediment were added under the authority of CWA Section 308(a) and 40 CFR Parts 

 122.41(j)(1), 122.43(a), and 122.48. 

16. Implementation of Source Controls

A. Implementation. The permittee shall continue to implement source control programs in each of the 

contributing basins in accordance with Chapter 40E-63, F.A.C., and other applicable programs. Basins that do 

not presently include source control programs shall be monitored to determine if such programs are necessary in

the event that phosphorus loads to the facility from these basins limit the facility’s ability to achieve the 

WQBEL.

B. Performance. On an annual basis, the permittee shall evaluate the performance of source controls in the 

contributing basins and include the findings in the annual report required by the permit. The report shall include 

phosphorus loads from the basins and shall describe trends and compare current loads to those determined 

necessary to achieve the WQBEL. 

C. Improvements. If the WQBEL is not achieved and if the assumed inflow concentration used to develop the 

Amended Determination remedy is exceeded, the permittee shall submit a report explaining the cause(s) for the 

excessive concentration and schedules and strategies for source control improvements necessary to achieve the 

WQBEL in the annual report. 

 This language or its equivalent was added as Section VII.G in the NPDES permits for 

 STAs 1E, 1W, 2, and 3/4, as Section VII.F in the NPDES permits for STAs 5 and 6, and 

 was modified in Specific Condition 10 of the STA 1E/1W EFA permit, Specific 

 Condition 13 of the STA 2 and 5/6 EFA permits, and Specific Condition 16 of the STA 

 3/4 EFA permit. Because the combination of source controls and STA treatment has 

 served as the foundation for Everglades restoration, this provision requires that source 

 control efforts continue, that progress be assessed and documented in the Annual Report, 

 and adds extra reporting requirements if the WQBEL is not achieved. These 

 requirements are based on Section 308(a) of the CWA. 

17. Annual Report Language 

The permittee shall submit an Annual Report demonstrating compliance with the conditions of this permit and 

according to the schedule in Section VI. The Annual Report shall provide details regarding the status of 

implementation of the requirements of this permit. Specifically, the report will include details regarding:

 a. Implementation of the WQBEL and activities required by this permit and affecting flows and loads to 

 STA-1W;

 b. Source control implementation and optimization; 

 c. STA design modifications affecting implementation of the WQBEL and activities required by this permit;

 d. Improvements, enhancements, and strategies that have been initiated and/or completed within the 

 previous year;

 e. Any delays in the implementation of the requirements of this permit, the duration of the delays, the 

 reason(s) for the delays, and the expected timeframe for their resolution;

 f. Whether revisions and/or additions to the requirements of this permit are recommended; 

g. The implementation status of STA Recovery Plans; 
8

h. For any noncompliance with permit conditions, an evaluation of the cause(s) and implementation of 

remedial measures; 

i. Whether the facility was operated within or outside of the operational envelope; and 

j. For each downstream transect station, a compilation of the water quality, sediment, and vegetation 

monitoring data collected, as appropriate, and an assessment of whether the cumulative impact 

remained unchanged, improved, or worsened from the previous year/monitoring.

 This language was added to, or made consistent between, Part I.E of the NPDES permits 

 for STA-1E, STA 2, STA 3/4, STA 5, and STA 6, Part I.C of the NPDES permit for 

 STA-1W, Specific Condition 26 of the STA-1E/1W EFA permit, Specific Condition 27 

 of the STA 2 EFA permit, Specific Condition 30 of the STA-3/4 permit, and Specific 

 Condition 28 of the STA-5/6 EFA permit. Item J above was added, where appropriate. 

III. Changed Provisions in Specific Permits 

A. STA 1E NPDES Permit 

1. Project Description 

The project is to construct, operate and maintain Stormwater Treatment Area 1E (STA-1E), the 

STA-1 Inflow and Distribution Works (STA-1 Inflow Basin), which includes the G-311, G-300, 

G-301, G-302, and S-5AS control structures, Inflow Pumping Station S-319, Inflow Pumping 

Station S-361, Gated Spillway G-311, STA-1E Works, Outflow Pumping Station S-362, C-51 

Basin Divide Structure S-155A, and C-51 Canal Improvements, collectively known as STA-1E. 

STA-1E is part of the Everglades Construction Project (ECP) construction, operation, and 

maintenance of which is required by the Everglades Forever Act (EFA) (Section 373.4592, F.S.). 

 This language was added to make it consistent with that in the EFA permit. Including the 

 Inflow Basin as part of the treatment works allows it to be covered by the bypass 

 provisions of the permit. 

2. Section VII.A.1 

The following documents (design documents), not attached hereto, but retained on file with the 

Department, are made a part hereof:

a. 1994 Conceptual Design Document for the Everglades Protection Project;

b. The June 13, 2000 Stormwater Treatment Area No 1 East Period of Record Dry-Out Analysis; 

c. The October, 1999 C-51 & STA 1 East Design Documentation Report; 

d. The January, 1999 Design Documentation Report, Canal 51 and Stormwater Treatment Area 1 East;
9

e. The May, 2000 Addendum To Design Documentation Report Stormwater Treatment Area 1 East;

f. The September 26, 2003 Stormwater Treatment Area, C-51 Improvements Construction and Solicitation 

Specifications; 

g. The February, 1999 C-51 West End Flood Control Project Final Environmental Impact Statement; and, 

h. The November 16, 2004 Everglades Protection Area Tributary Basins Long-Term Plan for Achieving 

Water Quality Goals.

 Because this section refers to projects specified in the Long-Term Plan that are now 

 deemed as non-conforming, USEPA deleted reference to them. 

3. Section VII.B.2 

Record drawings shall be prepared and made available in accordance with Rule 62-620.410(6), 

F.A.C., and the Department of Environmental Protection Guide to Wastewater Permitting within 

six months of placing the facilities into flow-through operation. 

 The Amended Determination remedies schedule and milestones are not based on the 

 historically used concept of flow-through operations. USEPA deleted that reference here. 

B. STA 1W NPDES Permit 

1. Section I.A.5 

By operation of the EFA, a numeric effluent limit for phosphorous shall be derived in accordance with state policy

as contained in the EFA, § 373.4592 (4) (e), Fla. Stat, which provides that if the Department does not adopt by rule a 

revised phosphorus water quality criterion by no later than December 31, 2003, the numeric criterion for phosphorus 

shall be 10 parts per billion (ppb) in the Everglades Protection Area. Upon adoption of a revised criterion or the 

default criterion becoming effective, and upon approval by EPA, an effluent limitation shall be established for this 

permit, in a manner consistent with the EPA, the federal Consent Decree in USA v. SFWMD, Case No. 88-1886-

CIV-HOEVELER, as may be modified, and other applicable state and federal laws and that recognizes the 

relationship between waters discharged to, and the resulting water quality in the Everglades Protection Area. If an 

effluent limitation is established for this permit based upon the default criterion, that effluent limitation will be 

replaced with a new effluent limit based on the approved numeric interpretation of the narrative phosphorous 

criterion once rulemaking for the phosphorous criterion and an appropriate effluent limitation is promulgated under 

the requirements of the EF A and the Consent Decree. The new effluent limit will be based on the numeric 

phosphorous criterion, the associated implementation strategy, and the relationship between waters discharged to, 

and the resulting water quality in, the Everglades Protection Area in a manner consistent with the EFA, the federal 

Consent Decree in USA v. SFWMD, Case No. 88-1886-CIV-HOEVELER, as may be modified, and other 

applicable state and federal laws. Persons whose substantial interests are affected by modification of this permit to 

include a new effluent limitation for phosphorus will be afforded a point of entry under Chapter 120, Florida 

Statutes

 This permit was last issued in 1999. This language was deleted since it pre-dates the 

 adoption and approval of the 10 ppb long-term geometric mean TP water quality 

 criterion. 
10

2. Section VII.E 

This permit currently contains the narrative water quality standard for nutrients. In accordance with Section 

373.4592(4)(e) or the Everglades Forever Act (EFA), by December 31, 2001, the Florida Department of 

Environmental Protection shall file a notice of rule making in the Florida Administrative Weekly to establish a 

phosphorus criterion in the Everglades Protection Area. By operation of the EFA, if the Department does not adopt 

by rule a revised phosphorus water quality criterion by December 31, 2003, the numeric criterion for phosphorus 

shall be the default of 10 ppb in the Everglades Protection Area. In either case, the numeric phosphorus criterion and 

implementation methodology must be submitted to EPA for approval. The USEPA shall review the water quality 

data that the state develops pursuant to the EFA, Section 373.4592(4)(e)l., Fla. Stat., and the interpreted numeric 

phosphorus criterion approved by the Florida Environmental Regulation Commission in accordance with the EFA, 

Section 373.4592( 4)(e)2., Fla. Stat., and shall approve the criterion provided it adequately protects the designated 

uses of the Everglades Protection Area, and complies with the Clean Water Act and implementing regulations. The 

same standard of review will apply to this criterion that applies to all other proposed State water quality standards.

In the event that the state of Florida revises the dissolved oxygen criterion, or establishes a site specific a1ternative 

criterion (SSAC) or other moderating provision for dissolved oxygen in the Everglades Protection Area., the 

numeric effluent limitation for dissolved oxygen contained in this permit shall be revised.

 This permit was last issued in 1999. This language was deleted since it pre-dates the 

 adoption and approval of the 10 ppb long-term geometric mean TP water quality 

 criterion. The last paragraph was deleted since it pre-dates the adoption and approval of 

 the DO SSAC. 

The permit shall be revised, or alternatively, revoked and reissued in accordance with the provisions contained in 

Rules 62-620.325 and 62-620.345 F.A.C., if applicable, or to comply with any applicable effluent standard or 

limitation issued or approved under Sections 301(b)(2)(C) and (D), 304(b)(2) and 307(a)(2) of the Clean Water Act 

(the Act), as amended, if the effluent standards, limitations, or water quality standards so issued or approved:

a. Contains different conditions or is otherwise more stringent than any condition in the permit/or;

b. Controls any pollutant not addressed in the permit.

The permit as revised or reissued under this paragraph shall contain any other requirements then applicable.

The permit may be reopened to adjust effluent limitations or monitoring requirements should future Water Quality 

Based Effluent Limitation determinations, water quality studies, DEP approved changes in water quality standards, or 

other information show a need for a different limitation or monitoring requirement.

The Department may develop a Total Maximum Daily Load (TMDL) during the life of the permit. Once a TMDL 

has been established and adopted by rule, the Department shall revise this permit to incorporate the final findings of 

the TMDL consistent with the requirements of Section 403.067, F.S.

 Since this NPDES permit was issued in 1999, these conditions were added to be 

 consistent with FDEP’s current permit reopener language. 

3. Section VII.F – Transect Monitoring 

 A second transect, the Z transect, was added based on recommendations from 

 Department of Interior scientists and USEPA’s consultant William Walker and the 

 authority of CWA Section 308(a). STA 1W discharges can go to the L-7 Canal, which 
11

 forms a topographic low point further downstream. Under certain hydrologic conditions, 

 that low point could discharge to the Refuge. 

 The Z transect impacted/unimpacted demarcation is based on: 

 Grover P, Bennet T, Weaver K, Nearhoof F, 2001. Everglades Phosphorus 

 Criterion Technical Support Document - Chapter 4.0-4.1: Results - Introduction 

 and Evidence of Phosphorus Enrichment. Florida Department of Environmental 

 Protection, Everglades Technical Support Section, Tallahassee, FL. Available at: 

 http://www.dep.state.fl.us/water/wqssp/everglades/pctsd.htm; Figure 4.1.5. 

4. Section VIII.V.1 

The term “bypass” does not include waters diverted around the entire STA-1W Project. Because 

of the hydrologic relationship between STA-1W and the Loxahatchee national Wildlife Refuge, 

“bypass” is not expected to occur at this facility.

 This language was stricken because it is not consistent with 40 CFR Part 122.41(m). 

C. STA 2 NPDES Permit 

1. Permit Cover Page 

This permit is accompanied by an Administrative Order (Order), AO-010-EV, pursuant to 

Subsections 403.088 (2)(e) and (f), F.S. Compliance with AO-010-EV is a specific requirement 

of this permit.

 Based on the 2008 and 2010 Orders, the AO compliance schedule is no longer valid 

 because it has the same effect as the invalidated portions of the Phosphorus Rule and the 

 EFAA. Because the conformed permit requires immediate compliance with the WQBEL, 

 all cites or links to a concurrent AO are being deleted. 

2. Section I.E.7 

Use of improvements, enhancements, and strategies identified

 This was deleted from several parts of this section because it appears to refer to non-

 conforming parts of the Long-Term Plan and/or the TBEL, which are no longer valid. 

D. STA 3/4 NPDES Permit 

1. Section I.A.5 

By operation of the EFA, a numeric effluent limit for phosphorus shall be derived in accordance with state policy as 

contained in the EFA, § 373.4592(4)(e), Fla. Stat., which provides that if the Department does not adopt by rule a 
12

revised phosphorus water quality criterion by no later than December 31, 2003, the numeric criterion for phosphorus 

shall be 10 parts per billion (ppb) in the Everglades Protection Area. Upon adoption of a revised criterion or the 

default criterion becoming effective, and upon approval by EPA, an effluent limitation shall be established for this 

permit, in a manner consistent with the EFA, the federal Consent Decree in USA v. SFWMD, Case No. 88-1886-

CIV-HOEVELER, as may be modified, and other applicable state and federal laws and that recognizes the 

relationship between waters discharged to, and the resulting water quality in the Everglades Protection Area. If an 

effluent limitation is established for this permit based upon the default criterion, that effluent limitation will be 

replaced with a new effluent limit based on the approved phosphorus numeric interpretation of the narrative 

phosphorus criterion once rulemaking for the phosphorus criterion and an appropriate effluent limitation is 

promulgated under the requirements of the EFA and the Consent Decree. The new effluent limit will be based on 

the numeric phosphorus criterion, the associated implementation strategy, and the relationship between waters 

discharged to, and the resulting water quality in, the Everglades Protection Area in a manner consistent with the 

EFA, the federal Consent Decree in USA v. SFWMD, Case No. 88-1886-CIV-HOEVELER, as may be modified, 

and other applicable state and federal laws. Persons whose substantial interests are affected by modification of this 

permit to include a new effluent limitation for phosphorus will be afforded a point of entry under Chapter 120, 

Florida Statutes. 

 This permit was last issued in 2004. This language was deleted since it pre-dates the 

 adoption and approval of the 10 ppb long-term geometric mean TP water quality 

 criterion. 

2. Section VII.E 

This permit currently contains the narrative water quality standard for nutrients. In accordance with Subsection 

373.4592(4)(e) of the Everglades Forever Act (EFA), the Florida Department of Environmental Protection filed a 

notice of rulemaking in the Florida Administrative Weekly to establish a phosphorus criterion in the Everglades 

Protection Area. By operation of the EFA, if the Department does not adopt by rule a revised phosphorus water 

quality criterion by December 31, 2003, the numeric criterion for phosphorus shall be the default of 10 ppb in the 

Everglades Protection Area. In either case, the numeric phosphorus criterion and implementation methodology must 

be submitted to EPA for approval. The USEPA shall review the water quality data that the state develops pursuant 

to the EFA, Subsection 373.4592(4)(e)1., Fla.Stat., and the interpreted numeric phosphorus criterion approved by 

the Florida Environmental Regulation Commission in accordance with the EFA, Subsection 373.4592(4)(e)2., 

Fla.Stat., and shall approve the criterion provided it adequately protects the designated uses of the Everglades 

Protection Area, and complies with the Clean Water Act and implementing regulations. The same standard of 

review will apply to this criterion that applies to all other proposed state water quality standards. 

In the event that the state of Florida revises the dissolved oxygen criterion, or establishes a site specific alternative 

criterion (SSAC) or other moderating provision for dissolved oxygen in the Everglades Protection Area, the numeric

effluent limitation for dissolved oxygen contained in this permit shall be revised.

 This permit was last issued in 2004. This language was deleted since it pre-dates the 

 adoption and approval of the 10 ppb long-term geometric mean TP water quality 

 criterion. The last paragraph was deleted since it pre-dates the adoption and approval of 

 the DO SSAC. 

The permit shall be revised, or alternatively, revoked and reissued in accordance with the provisions contained in 

Rules 62-620.325 and 62-620.345 F.A.C., if applicable, or to comply with any applicable effluent standard or 

limitation issued or approved under Sections 301(b)(2)(C) and (D), 304(b)(2) and 307(a)(2) of the Clean Water Act 

(the Act), as amended, if the effluent standards, limitations, or water quality standards so issued or approved:

a. Contains different conditions or is otherwise more stringent than any condition in the permit/or;

b. Controls any pollutant not addressed in the permit.
13

The permit as revised or reissued under this paragraph shall contain any other requirements then applicable.

The permit may be reopened to adjust effluent limitations or monitoring requirements should future Water Quality 

Based Effluent Limitation determinations, water quality studies, DEP approved changes in water quality standards, or 

other information show a need for a different limitation or monitoring requirement.

The Department may develop a Total Maximum Daily Load (TMDL) during the life of the permit. Once a TMDL 

has been established and adopted by rule, the Department shall revise this permit to incorporate the final findings of 

the TMDL consistent with the requirements of Section 403.067, F.S.

 Since this NPDES permit was issued in 2004, these conditions were added to be 

 consistent with FDEP’s current permit reopener language. 

3. Section VII.F 

This permit does not authorize the hydropattern restoration of WCA-3A. Once the performance 

of STA-3/4 has been optimized and long-term water quality solutions for S-7/S-2 and S-8/S-3 

basins have been implemented attains the WQBEL, it is anticipated that discharges from STA3/4 will be diverted directly into WCA-3A could be directed southward directly across the L-5 

canal and levee into WCA-3A to assist in hydropattern restoration in accordance with Subsection 

(4)(b) of the EFA. Future WCA-3A hydropattern restoration plans will be coordinated with 

CERP implementation. Implementation of hydropattern restoration in WCA-3A associated with 

STA-3/4 will require review and approval by the Department and USEPA in the form of a 

modification to this permit. If hydropattern restoration proceeds, monitoring will be required 

along a transect in WCA3A downstream of the STA 3/4 discharge. The purpose of this 

monitoring will be to document the effect of the discharge on the downstream EPA marsh and 

changes in downstream water quality and cumulative phosphorus impacts. Transect monitoring 

will begin one year prior to the commencement of hydropatterm restoration discharges in order 

to document baseline conditions. The modification will require downstream monitoring which 

must be implemented sufficiently in advance to establish a scientifically-defensible baseline and 

may include transect monitoring, if appropriate. The monitoring plan should be submitted to the 

Department for review and approval prior to the commencement of monitoring.

 

 This provision was conformed to reflect the 2010 Order requirements regarding 

 implementation of the WQBEL and to assess possible future changes in downstream 

 water quality and cumulative phosphorus impacts in the Everglades. 

4. Section VIII.22 

The term “bypass” does not include waters diverted around the entire STA-3/4 project via the G371 and G-373 structures, to prevent damage to the facility (usually caused by flooding) or for 

water resource needs such as the prevention of adverse impacts to public and/or environmental 

health as described in Condition b. below. 

 This language was stricken because it is not consistent with 40 CFR Part 122.41(m). 
14

E. STA 5 NPDES Permit 

1. Permit Cover Page 

This permit is accompanied by an Administrative Order (Order), AO-011-EV, pursuant to 

Subsections 403.088 (2)(e) and (f), F.S. Compliance with AO-011-EV is a specific requirement 

of this permit.

 Based on the 2008 and 2010 Orders, the AO compliance schedule is no longer valid 

 because it has the same effect as the invalidated portions of the Phosphorus Rule and the 

 EFAA. Because the conformed permit requires immediate compliance with the WQBEL, 

 all cites or links to a concurrent AO are being deleted. 

2. Section I.E.7 

Use of improvements, enhancements, and strategies identified

 This was deleted from several parts of this section because it appears to refer to non-

 conforming parts of the Long-Term Plan and/or TBELs, which are no longer valid. 

F. STA 6 NPDES Permit 

1. Permit Cover Page 

This permit is accompanied by an Administrative Order (Order), AO-012-EV, pursuant to 

Subsections 403.088 (2)(e) and (f), F.S. Compliance with AO-012-EV is a specific requirement 

of this permit.

 Based on the 2008 and 2010 Orders, the AO compliance schedule is no longer valid 

 because it has the same effect as the invalidated portions of the Phosphorus Rule and the 

 EFAA. Because the conformed permit requires immediate compliance with the WQBEL, 

 all cites or links to a concurrent AO are being deleted. 

2. Section I.E.7 

“Use of improvements, enhancements, and strategies identified”

 This was deleted from several parts of this section because it appears to refer to non-

 conforming parts of the Long-Term Plan and/or TBELs, which are no longer valid. 
15

G. STA 1E/1W EFA Permit 

1. General Condition 2 

Scope of permit. This permit is valid only for the specific processes and operations applied for 

and indicated in the approved drawings or exhibits requirements of this permit. Any 

unauthorized deviation from the approved drawings, exhibits, specifications, or conditions

requirements of this permit may constitute grounds for revocation and enforcement action by the 

Department. 

 

 This section is conformed to ensure that all references to non-conforming elements of the 

 Long Term Plan are stricken, consistent with the requirements of the 2010 Order and the 

 Amended Determination. 

2. General Condition 5 

Liability. This permit does not relieve the permittee from liability for harm or injury to human 

health or welfare, animal, or plant life, or property caused by the construction or operation of this 

permitted source, or from penalties therefore; nor does it allow the permittee to cause pollution in 

contravention of Florida Statutes and Department rules, unless specifically authorized by an 

order from the Department. The permittee shall hold and save the Department harmless from 

any and all damages, claims, or liabilities which may arise by reason of the construction, 

alteration, operation, maintenance, removal, abandonment or use of any system authorized by the 

permit. 

 The 2010 Order has currently enjoined FDEP from modifying NPDES permits through 

 EFA permits (or AOs). 

3. Specific Conditions 14 and 15 

14. Stabilization Phase (Flow-through Operations) – During the Stabilization Phase the treatment vegetation will be 

maturing and the STA performance will generally be improving toward achieving the TBEL. However, the overall 

performance of the STA is extremely difficult to evaluate and predict. It is anticipated that the treatment vegetation 

may require one to three years after flow-through operations begin for the affected cells to achieve optimal 

performance. During the stabilization phase the TBEL shall apply. Once the facility achieves the TBEL it shall 

enter the Routine Operations Phase. During the Stabilization Phase, exceedance of the TBEL may occur; however, 

the STA shall be deemed in compliance with the permit as long as the actions described Specific Condition 17 of 

this permit are being taken in conjunction with all other applicable permit conditions.

An STA or Flow-way may enter the Stabilization Phase after one of four antecedent conditions: (1) once flowthrough operations begin following the initial start-up of a new treatment cell; (2) when a treatment cell is taken offline for implementation of Long-Term Plan enhancements that may have adverse impacts on STA performance, (3) 

when a treatment cell is taken off-line for recovery activities associated with a major event that compromises the 

structural integrity or performance of the STA, or (4) planned/unplanned maintenance activities which would cause 

adverse impacts to the STA’s treatment capabilities. If the flow-way is determined by the District to be incapable of 

operating or performing effectively as a result of the impacts caused by one or more of these circumstances, the 

District shall submit strategies and timelines identified as being the most effective in restoring the impacted flowway(s) to the optimal performance level within 60 days from such a determination or occurrence. The timely 

submittal and implementation of these strategies and timelines in conjunction with the Department’s review and 
16

approval of such submittals and compliance with all other applicable conditions of this permit shall constitute 

compliance. 

As part of the first annual report following any adverse impact to the facility, and each subsequent year until the 

facility achieves the TBEL, the 12 month rolling flow-weighted mean TP concentration of the STA outflow shall be 

assessed as to whether there is a trend in improvement of performance relative to prior years. If the trend analysis 

that is applied to this data indicates that there is not a trend in improvement of performance, the permittee shall 

report as to the causes behind the lack of performance improvement. If during a subsequent annual report the trend 

analysis applied to these data indicate that there is not a trend in improvement of performance after the affected 

flow-way has been in flow-through operation for 24 months, the annual report shall include any remedial measures 

necessary to achieve improved facility performance by the end of next year, and shall provide an estimate of when 

the TBEL shall be achieved. 

154. Routine Operations Phase - During the Routine Operations Phase, discharges from the STAs shall achieve 

compliance with the WQBEL as of December 31, 2006. TBEL, as described in Specific Condition 16 of this permit. 

STA-1W and STA-1E shall achieve the WQBEL, established pursuant to Specific Condition 18, by no later than 

Dec 31, 2016. 

USEPA recognizes that time is needed from when flooding occurs and 

 emergent/submerged/floating vegetation begins to function until the WQBEL is 

 achieved. However, reliance on the historically used concepts of ‘stabilization’ and 

 ‘flow-through operations’ is no longer needed. Because use of stabilization had been 

 linked to TBEL compliance and since the 2010 Order deems the use of TBELs to be 

 invalid, continued regulatory application of stabilization is not appropriate. 

4. Specific Condition 16

Application of Technology Based Effluent Limits. The TBEL described above will be applied as follows: 

A. Compliance shall be tested in each water year (May – April) using data from the monitored representative 

inflow structures (G-302, G-311, and S-319) and outflow structures (G-251, G-310, and S-362), except as 

noted below. The result of this compliance testing shall be reported by the District as part of the annual 

reporting requirements in Specific Condition 30. The compliance calculations will exclude flows made for 

low flow water supply deliveries. Low flow water supply deliveries are deliveries that pass through the 

Everglades Protection Area to Dade, Broward or Palm Beach County, and the Big Cypress Seminole Indian 

Reservation for water supply (wellfield recharge and salt water intrusion prevention) purposes. In addition, 

low flow water supply deliveries are made at times when water levels in the Water Conservation Areas 

(WCAs) are below the minimum elevations presented below: 

• WCA-1 – 14.5 ft. NGVD measured at the 1-8C gauge 

• WCA-2 – 10.5 ft. NGVD measured at the headwater (HW) of the S-11B structure 

• WCA-3A – 7.5 ft. NGVD measured at HW of S-333 or 11.0 ft at HW of G-409 

These stage thresholds will be reviewed as part of any future analyses associated with revisions to the 

current regulation schedules (WCA-1: May 1995; WCA-2: June 1989; WCA-3A: November 2000). This 

method will also exclude water supply deliveries to the Loxahatchee National Wildlife Refuge (Refuge) or 

Everglades National Park (ENP), which have been requested by Refuge, ENP or U.S. Army Corps of 

Engineers staff and which cannot be treated by an STA prior to delivery. 

B. The TBEL shall not apply in water years when rainfall in the source basins tributary to the STA exceeds the 

maximum annual basin rainfall that occurred during the period of record used for deriving the TBEL (See 

Goforth et. al., 2007). In addition, the TBEL shall not apply in water years when rainfall in the basin 

tributary to that STA is less than the minimum annual rainfall that occurred during the period of record 

used for deriving the TBEL for that STA if supplemental flows are not available to maintain wet conditions 
17

in that STA. If a year is excluded based upon these criteria, results from adjacent years shall be treated as 

consecutive in testing compliance. 

C. The STAs will be deemed in compliance with the TBEL unless the annual flow-weighted mean phosphorus 

concentration at the monitored representative outflows is greater than the annual limit. The annual limit can 

be calculated using the methods contained on pages 9-12 of the Technical Support Document for the STA1W TBEL (Goforth et al. 2007, Exhibit B) and the Technical Support Document for the STA-1E TBEL

(Goforth et. al., 2007, Exhibit C). The method may be revised in the future as appropriate to reflect lower 

STA limits. Tables 2 and 3 below contain example calculations of the TBEL based on corresponding 

phosphorus loading rates (PLR). 

 Based on the 2010 Order, the use of TBELs is no longer valid because they derive 

 from non-conforming parts of the Long-Term Plan and are also considered 

 moderating provisions. 

5. Specific Condition 2319

Factors Outside the Permittee’s Control. In the event that non-compliance or failure to achieve the WQBEL

performance objectives results for any of the reasons other than those below, the permittee shall take appropriate 

remedial measures. 

A. Anomalous Rainfall. Compliance with the TBEL shall not be tested in water years when the rainfall in the 

source basins exceed the range of values that occurred during the period of model simulation used in the 

development of the TBELs, or when sufficient supplemental flows are not available to maintain an average 

depth of 0.5 ft in each treatment cell of STA-1W and/or STA-1E. In these instances, results from adjacent 

years will be treated as consecutive for purposes of testing compliance. The Department may make similar 

adjustments where emergency discharges occur.

B. Random Variation. The permittee shall report any statistical uncertainty in the methodology using 

acceptable scientific methods.

 Factor A above was stricken because it relates to TBELs, which derive from non-

 conforming parts of the Long-Term Plan and are also considered moderating provisions. 

 Factor B was stricken because it is an inappropriate basis to avoid the consequences of 

 WQBEL non-compliance. 

6. Specific Condition 261

A. STA-1W Diversion Limit. To limit discharge concentrations resulting from diversion events, discharges 

of waters from the EAA to the L-7 Canal from the G-301 diversion structure and the discharge pump 

stations from STA-1W shall not exceed a 50 ppb maximum annual discharge limit. The 50 ppb maximum 

annual discharge limit shall be calculated as an annual flow weighted mean total phosphorus concentration 

for combined discharges from the EAA during the May-April Water Year from the G-301 diversion 

structures and from the G-251 and G-310 pump stations. 

B. STA-1E Diversion Limit. To limit discharge concentrations resulting from diversion events, discharges of 

waters from the EAA to the L-40 Canal from the G-300 diversion structure and the discharge pump station 

from STA-1E shall not exceed a 50 ppb maximum annual discharge limit. The 50 ppb maximum annual 

discharge limit shall be calculated as an annual flow weighted mean total phosphorus concentration for 

combined discharges from the EAA during the May-April Water Year from the G-300 structure and the G362 pump station.
18

The 50 ppb maximum annual discharge limit for waters from the EAA shall be enforceable after all of the additional 

components of the control program set forth in Specific Condition 17 of this permit are operational. By including a 

50 ppb maximum annual discharge limit in this permit, the Department is not determining, admitting, or waiving 

any adjudicating permittee’s or the Department’s rights, claims, or defenses of the permittee, the Department, or any 

other party to any matters relating to compliance with requirements of the Everglades Consent Decree, as modified, 

entered in the case styled United States v. So. Fla. Water Management Dist., et al., case No. 88-1886-CIV-Moreno 

(S.D. Fla.).

 Because the WQBEL is effective immediately, this language has been deleted. 

7. Specific Condition 3026.C.1 

Records of the operations status of the STAs during the water year, stating whether each STA (or 

particular cells or flow-ways therein) is in start-up, stabilization or routine operations; 

 As explained above, since the concept of ‘stabilization’ has been linked to TBELs and 

 is no longer appropriate, this was stricken. Information regarding start-up is needed 

 since remedy milestone dates are in part, based on that. 

8. Specific Condition 3026.E.6 

The operational status of the STA, stating whether the STA is in routine operations or start-up

stabilization. If the facility is in non-routine operations during the reporting period, the report 

shall also include the date at which the facility entered the start up or stabilization phase and the 

length of time it remained or is expected to remain in that phase; 

 As explained above, since the concept of ‘stabilization’ has been linked to TBELs and 

 is no longer appropriate, this provision was stricken. Information regarding start-up is 

 needed since remedy milestone dates are in part, based on that. 

9. Tables 2 and 3 - Interim TBELs for STA-1W and STA-1E As A Function of PLR 

 Based on the 2010 Order, these tables are stricken because the use of TBELs is no longer 

 valid since they derive from non-conforming parts of the Long-Term Plan and are also 

 considered moderating provisions. 

H. STA 2 EFA Permit 

 

1. Permit Cover Page 

This permit is accompanied by Administrative Order AO-010-EV, which is incorporated herein 

by reference. 

 Based on the 2008 and 2010 Orders, the AO compliance schedule is no longer valid 

 because it has the same effect as the invalidated portions of the Phosphorus Rule and the 

 EFAA. Because the conformed permit requires immediate compliance with the WQBEL, 

 all cites or links to a concurrent AO are being deleted. 
19

2. General Condition 2 

Scope of permit. This permit is valid only for the specific processes and operations applied for 

and indicated in the approved drawings or exhibits requirements of this permit. Any 

unauthorized deviation from the approved drawings, exhibits, specifications, or conditions

requirements of this permit may constitute grounds for revocation and enforcement action by the 

Department. 

 This section is conformed to ensure that all references to non-conforming elements of the 

 Long Term Plan are stricken, consistent with the requirements of the 2010 Order and the 

 Amended Determination. 

3. General Condition 5 

Liability. This permit does not relieve the permittee from liability for harm or injury to human 

health or welfare, animal, or plant life, or property caused by the construction or operation of this 

permitted source, or from penalties therefore; nor does it allow the permittee to cause pollution in 

contravention of Florida Statutes and Department rules, unless specifically authorized by an 

order from the Department. The permittee shall hold and save the Department harmless from 

any and all damages, claims, or liabilities which may arise by reason of the construction, 

alteration, operation, maintenance, removal, abandonment or use of any system authorized by the 

permit. 

 The 2010 Order has currently enjoined FDEP from modifying NPDES permits through 

 EFA permits (or AOs). 

4. Specific Conditions 18 and 19 

Stabilization Phase. (Flow-through Operations)– An STA enters the Stabilization Phase after each of three 

antecedent conditions: (1) once flow-through operations begin following the initial start-up of a new treatment cell; 

(2) when a treatment cell is underoing implementation of the Long-Term Plan enhancements that may have adverse

impacts on STA performance, or (3) when a treatment cell undergoing recovery activities associated with a major 

event that compromises the structural integrity or performance of the STA. During the Stabilization Phase the

treatment vegetation will be maturing and the STA performance will generally be improving toward achieving the

permit effluent limitation. However, the overall performance of the STA is extremely difficult to evaluate and 

predict. It is anticipated that the treatment vegetation will require one to three years after flow-through operations 

begin for the affected cells to continue to improve toward achieving the permit effluent limit. During the 

stabilization phase, the effluent limitation shall apply. Once the facility achieves the effluent limitation, it shall enter 

the Routine Operations Phase. During the Stabilization Phase, exceedance of the effluent limitation is anticipated; 

however, the STA shall be deemed in compliance as long as the actions described in this condition and all other 

applicable permit conditions are met. 

If a flow-way is determined to be incapable of operating or performing effectively as a result of the impacts caused 

by one or more of the above mentioned circumstances, within 60 days the District shall submit strategies and 

timelines identified as being the most effective in restoring the impacted flow-way(s) and achieving the permit 

effluent limit. The District’s strategies and timelines shall include, at a minimum, the following:

1. Identify the cause of the incident which resulted in the facility not achieving the effluent limitation;

2. A statement that the facility was being properly operated at the time of the incident;

3. The period of the anticipated stabilization phase; and,
20

4. Any remedial steps employed to ensure that the stabilization period will be as minimal as possible..

The timely submittal and implementation of these strategies and timelines in conjunction with the Department’s 

review and approval of such submittals and compliance with all other applicable conditions set forth in this permit 

shall constitute compliance. 

In addition to the reporting associated with this condition and as part of the annual reporting requirements of the 

permit, the District shall provide an assessment of the facility and the steps taken to meet the permit effluent limit. 

As part of the first annual report following any adverse impact to the facility, and each subsequent year until the 

facility achieves the permit effluent limit, the 12 month rolling flow weighted mean TP concentration of the STA

outflow shall be assessed as to whether there is a trend in improvement of performance relative to prior years. If the 

trend analysis that is applied to this data indicates that there is not a trend in improvement of performance, the 

permittee shall report as to the causes behind the lack of performance improvement. If during a subsequent annual 

report the trend analysis applied to these data indicate that there is not a trend in improvement of performance after 

the affected flow-way has been in flow-through operation for 24 months, the annual report shall include any 

remedial measures necessary to achieve improved facility performance by the end of next year, and shall provide an 

estimate of when the permit effluent limit shall be achieved. 

1918. Routine Operations Phase. During the Routine Operations Phase, discharges from the STA 

shall meet the WQBEL permit effluent limitations set forth in Table 1 below. 

USEPA recognizes that time is needed from when flooding occurs and 

 emergent/submerged/floating vegetation begins to function until the WQBEL is 

 achieved. However, reliance on the historically used concepts of ‘stabilization’ and 

 ‘flow-through operations’ is no longer needed. Because use of stabilization had been 

 linked to TBEL compliance and since the 2010 Order deems the use of TBELs to be 

 invalid, continued regulatory application of stabilization is not appropriate. 

5. Specific Condition 2120

Factors Outside the Permittee’s Control. In the event that non-compliance or failure to achieve performance 

objectives results for any of the reasons other than those below, the permittee shall take appropriate remedial 

measures.

A. Anomalous Rainfall. Compliance with the effluent limitation shall not be tested in water years when the 

rainfall in the source basins fall outside the range of values that occurred during the period of model simulation 

if sufficient supplemental flows are not available to maintain wet conditions in STA-2. A joint field inspection 

between the Department and the District will be undertaken to verify if the facility has resulted in dryout 

conditions that would impact compliance. In these instances, results from adjacent years will be treated as 

consecutive for purposes of testing compliance. The Department may make similar adjustments where 

emergency discharges occur.

B. Random Variation. The permittee shall report any statistical uncertainty in the methodology using 

acceptable scientific methods.

 Factor A above was stricken because reporting on whether the facility operated within or 

 outside the operational envelope will provide equivalent information. Factor B was 

 stricken because it is an inappropriate basis to avoid the consequences of WQBEL non-

 compliance. 
21

6. Specific Condition 278.C 

Performance Evaluation. The Annual Report shall provide a performance evaluation for STA-2 

containing the following information: The operations status of the STA, stating whether the 

STA is in start-up, stabilization or routine operations. 

 As explained above, since the concept of ‘stabilization’ is no longer valid, this 

 provision has been stricken. Information regarding start-up is needed since remedy 

 milestone dates are in part, based on that. 

7. Specific Condition 30.D.6 

The operational status of the STA, stating whether the STA is in Start-up, Stabilization or Routine Operations.; If 

the facility is in Stabilization operations during the reporting period, the report shall also include the date at which 

the facility entered the Stabilization Phase and the length of time it remained or is expected to remain in that phase

 As explained above, since the concept of ‘stabilization’ is no longer valid, this 

 provision has been stricken. Information regarding start-up is needed since remedy 

 milestone dates are in part, based on that. 

I. STA 3/4 EFA permit 

1. Project Description 

A stabilization phase will follow, continuing until the 12 month flow-weighted average total 

phosphorus concentration at the outflow is less than or equal to 50 parts per billion. Thereafter, 

the project will be in the normal or post stabilization operations phase. Once the WQBEL is 

achieved, the project will be in routine operations.

 USEPA recognizes that time is needed from when flooding occurs and 

 emergent/submerged/floating vegetation begins to function until the WQBEL is 

 achieved. However, reliance on the historically used concept of ‘stabilization’ is no 

 longer needed. Because use of stabilization had been linked to TBEL compliance and 

 since the 2010 Order deems the use of TBELs to be invalid, continued regulatory 

 application of ‘stabilization’ is not appropriate. The concept of ‘routine operations’ 

 was added to be consistent with the other EFA permits. 

2. General Condition 2 

Scope of permit. This permit is valid only for the specific processes and operations applied for 

and indicated in the approved drawings or exhibits requirements of this permit. Any 

unauthorized deviation from the approved drawings, exhibits, specifications, or conditions

requirements of this permit may constitute grounds for revocation and enforcement action by the 

Department. 

 
22

 This section is conformed to ensure that all references to non-conforming elements of the 

 Long Term Plan are stricken, consistent with the requirements of the 2010 Order and the 

 Amended Determination. 

3. Specific Condition 10.G 

Operational Envelope. The permittee shall ensure to the maximum extent practicable that 

authorized operation of the existing components of the facility do not exceed the operational 

envelope for STA-3/4, as set forth in the existing STA-3/4 Operations Plan. 

 This language was added to make it consistent with the other NPDES and EFA permits. 

4. Specific Condition 16 

Stabilization. Following completion of the Start-Up Phase, the project shall begin a period of stabilization, in 

accordance with Subsection (9)(h) of the EFA. The stabilization period for STAs is generally anticipated to last 2 to 

3 years after the start-up phase ends. During that period, compliance with the criteria in Subsection (9)(h) of the 

EFA shall be evaluated as follows:

After start-up operations have ended and flow project flow-through operations and discharges have begun from each 

flow-way, the District shall operate and monitor STA-3/4, allowing for a stabilization period. The stabilization 

period for STA-3/4 shall end when the 12 month flow-weighted average total phosphorus concentration at the 

outflow stations is less than or equal to 50 ppb. Starting 12 months after commencing discharge from each flowway, the District shall provide rolling 12 month flow-weighted average total phosphorus concentration in monitoring 

reports. If, after the first two years of full project flow-through operation, the STA has not met this stabilization test, 

the District shall submit a report which shall compare the flow weighted mean of the total phosphorus discharge data 

from the most recent 12-month period (e.g., months 13 - 24) with the flow-weighted mean of the total phosphorus 

discharge data from the previous 12 month period (e.g., months 1 - 12) to ensure that performance of the STA is not 

declining, based upon a Student’s t-test at the 95% confidence interval. This report is to be submitted 90 days after 

the end of each reporting period. If at any time, the STA performance indicates that this test will not be met by 

December 31, 2006, the permittee shall submit a report on the progress made towards meeting the stabilization 

requirements and an analysis of the system operation and shall submit and initiate implementation of an 

optimization plan designed to reach the phosphorus stabilization goal by December 31, 2006.

 USEPA recognizes that time is needed from when flooding occurs and 

 emergent/submerged/floating vegetation begins to function until the WQBEL is 

 achieved. However, reliance on the historically used concepts of ‘stabilization’ and 

 ‘flow-through operations’ is no longer needed. Because use of stabilization had been 

 linked to TBEL compliance and since the 2010 Order deems the use of TBELs to be 

 invalid, continued regulatory application of stabilization is not appropriate.

5. Specific Condition 17 

Post Stabilization / Normal Flow-Through Operations. From the end of the stabilization period, until the 

beginning of the long-term compliance period discharges from STA-3/4, via the G-376B, G-376E, G-379B, G379D, G-381B, and G-381E structures, shall meet an annual flow-weighted average total phosphorus concentration 

at the outflow stations of less than or equal to 76 ppb for each water year, (May 1 - April 30). In addition, the 

discharges shall not exceed an annual flow weighted average total phosphorus concentration of 50 ppb for three or 

more consecutive water years. Both tests are simultaneously applied to ensure that the design objectives of the 

STA-3/4 project are met.
23

 Based on the 2010 Order, the use of TBELs is no longer valid because they derive from 

 non-conforming parts of the Long-Term Plan and are also considered moderating 

 provisions. USEPA deems this provision to set TBELs and has stricken it accordingly. 

6. Specific Condition 221

Factors Outside the Permittee’s Control. In the event that non-compliance or failure to achieve the WQBEL

performance objectives results for any reason other than those listed below, the permittee shall take appropriate 

remedial measures. 

A. Anomalous Rainfall. Compliance with Specific Conditions 16-19 shall not be tested in water years 

when the EAA annually adjusted rainfall, as defined in Rule 40E-63, F.A.C., exceeds 63.8 inches, or is less 

than 35.1 inches (based on the minimum and maximum annual rainfall values for the EAA during water 

years 1979 thru 1988), and sufficient supplemental flows are not available to maintain wet conditions in 

STA-3/4. In this instance, results from adjacent years will be treated as consecutive for purposes of testing 

compliance. The Department may make similar adjustments where emergency discharges occur. 

B. Natural Background. Deviations from water quality standards may occur as a result of natural 

background conditions, in accordance with Section 403.021(11), F.S. The Department shall evaluate such 

deviations as a part of the Department’s evaluation of water quality standards in accordance with 

Subsection (4)(e)4 of the EFA.

C. Random Variation. The District shall report any statistical uncertainty in the methodology using 

acceptable scientific methods.

D. Vegetation Conditions. The District shall report whether vegetation conditions in STA-3/4 have 

contributed to the non-compliance. The permittee shall prepare an analysis of the vegetation coverage 

of STA-3/4 as compared with the baseline vegetation coverage maps developed in accordance with the 

monitoring conditions found in Specific Condition 29.

 Factor A above was stricken because reporting on whether the facility operated within or 

 outside the operational envelope will provide equivalent information. Factor B was 

 stricken because it is not appropriate to apply a natural background condition to TP 

 levels in wastewater coming into the STAs for treatment. Factors C and D were stricken 

 because they are inappropriate bases to avoid the consequences of WQBEL non-

 compliance. 

7. Specific Condition 30.D 

Performance Evaluation. 

1. The operations status of the STA, stating whether the STA is in start-up, stabilization, or normal flowthrough routine operations; 

2. A comparison of inflow water quality data with outflow water quality data using the student’s t-test 

with a 95% confidence intervals; and, 

3. Beginning with the second Annual Report, a A comparison of performance of current reporting year 

with performance in previous years. 

 As explained above, since the concept of ‘stabilization’ is no longer valid, this provision 

 has been stricken. 
24

8. Specific Condition 30.F 

Item 6. The operational status of the STA, stating whether the STA is in routine operations or start-up stabilization. 

If the facility is in start-up non-routine operations during the reporting period, the report shall also include the date 

at which the facility entered start up or stabilization phase and the length of time it remained or is expected to remain 

in that phase; Achievement of effluent limitations set forth in the TBEL and/or 

 As explained above, since the concept of ‘stabilization’ is no longer valid, this provision 

 has been stricken. Information regarding start-up is needed since remedy milestone dates 

 are in part, based on that. 

J. STA 5/6 EFA permit 

1. Cover Page 

This permit is accompanied by Administrative Order AO-011-EV, which is incorporated herein 

by reference.

 Based on the 2008 and 2010 Orders, the AO compliance schedule is no longer valid 

 because it has the same effect as the invalidated portions of the Phosphorus Rule and the 

 EFAA. Because the conformed permit requires immediate compliance with the WQBEL, 

 all cites or links to a concurrent AO are being deleted. 

2. Scope of permit. This permit is valid only for the specific requirements of this permit processes and operations 

applied for and indicated in the approved drawings or exhibits. Any unauthorized deviation from the approved 

drawings, exhibits, specifications, or conditions requirements of this permit may constitute grounds for revocation 

and enforcement action by the Department. 

This section is conformed to ensure that all references to non-conforming elements of the 

 Long Term Plan are stricken, consistent with the requirements of the 2010 Order and the 

 Amended Determination. 

3. Specific Condition 18 

Stabilization Phase (Flow-through Operations)– An STA enters the Stabilization Phase after each of three 

antecedent conditions: (1) once flow-through operations begin following the initial start-up of a new treatment cell; 

(2) when a treatment cell is undergoing implementation of Long-Term Plan enhancements that may have adverse 

impacts on STA performance, or (3) when a treatment cell undergoing for recovery activities associated with a 

major event that compromises the structural integrity or performance of the STA. During the Stabilization Phase the 

treatment vegetation will be maturing and the STA performance will generally be improving toward achieving the 

permit effluent limitation. However, the overall performance of the STA is extremely difficult to evaluate and 

predict. It is anticipated that the treatment vegetation will require one to three years after flow-through operations 

begin for the affected cells to continue to improve toward achieving the permit effluent limit. During the 

stabilization phase the effluent limitation shall apply. Once the facility achieves the effluent limitation it shall enter 

the Routine Operations Phase. During the Stabilization Phase, exceedance of the effluent limitation is anticipated; 

however, the STA shall be deemed in compliance as long as the actions described in this condition and all other 

applicable permit conditions are met. 

If a flow-way is determined to be incapable of operating or performing effectively as a result of the impacts caused 

by one or more of the above mentioned circumstances, within 60 days the District shall submit strategies and 
25

timelines identified as being the most effective in restoring the impacted flow-way(s) and achieving the permit 

effluent limit. The District’s strategies and timelines shall include, at a minimum, the following:

1. Identify the cause of the incident which resulted in the facility not achieving the effluent limitation;

2. A statement that the facility was being properly operated at the time of the incident;

3. The period of the anticipated stabilization phase; and,

4. Any remedial steps employed to ensure that the stabilization period will be as minimal as possible..

The timely submittal and implementation of these strategies and timelines in conjunction with the Department’s

review and approval of such submittals and compliance with all other applicable conditions set forth in this

permit shall constitute compliance

 USEPA recognizes that time is needed from when flooding occurs and 

 emergent/submerged/floating vegetation begins to function until the WQBEL is 

 achieved. However, reliance on the historically used concepts of ‘stabilization’ and 

 ‘flow-through operations’ is no longer needed. Because use of stabilization had been 

 linked to TBEL compliance and since the 2010 Order deems the use of TBELs to be 

 invalid, continued regulatory application of stabilization is not appropriate. 

As part of the first annual report following any adverse impact to the facility, and each subsequent year until the 

facility achieves the permit effluent limit, the 12 month rolling flow-weighted mean TP concentration of the STA 

outflow shall be assessed as to whether there is a trend in improvement of performance relative to prior years. If the 

trend analysis that is applied to this data indicates that there is not a trend in improvement of performance, the 

permittee shall report as to the causes behind the lack of performance improvement. If during a subsequent annual 

report the trend analysis applied to these data indicate that there is not a trend in improvement of performance after 

the affected flow-way has been in flow-through operation for 24 months, the annual report shall include any 

remedial measures necessary to achieve improved facility performance by the end of next year, and shall provide an 

estimate of when the permit effluent limit shall be achieved.

The Annual Report requirements in Specific Condition 28.D has been conformed to 

require that the specific cause(s) for delay in WQBEL implementation and timeframes for 

resolution be provided. In light of those requirements, this provision is not relevant or 

appropriate. 

4. Specific Condition 21 

Factors Outside the Permittee’s Control. In the event that non-compliance or failure to achieve the WQBEL 

performance objectives results for any of the reasons other than those below, the permittee shall take appropriate 

remedial measures. 

A. Anomalous Rainfall. Compliance with the effluent limitation shall not be tested in water years when the 

rainfall in the source basins fall outside the range of values that occurred during the period of model 

simulation if sufficient supplemental flows are not available to maintain wet conditions in STA-5/6. A 

joint field inspection between the Department and the District will be undertaken to verify if the facility has 

resulted in dryout conditions that would impact compliance. In these instances, results from adjacent years 

will be treated as consecutive for purposes of testing compliance. The Department may make similar 

adjustments where emergency discharges occur.

B. Random Variation. The permittee shall report any statistical uncertainty in the methodology using 

acceptable scientific methods.
26

Factor A above was stricken because reporting on whether the facility operated within or 

outside the operational envelope will provide equivalent information. Factor B was 

stricken because it is an inappropriate basis to avoid the consequences of WQBEL noncompliance. 

 

5. Specific Condition 28.C 

Performance Evaluation. The Annual Report shall provide a performance evaluation for STA-5/6 containing the 

following information: 

1. The operations status of the STA, stating whether the STA is in start-up, stabilization or routine 

operations 

2. A comparison of inflow water quality data with outflow water quality data an appropriate statistical 

test with a 95% confidence interval and based on statistical distributional assumptions (e.g., Student's 

t-test or Mann-Whitney test); 

3. A comparison of outflow phosphorus concentrations with the permit effluent limit for STA-5/6 and 

 between the current reporting year and previous years 

4. An assessment of the inflow volumes and phosphorus loads during the year relative to the anticipated 

 operational envelope contained in the STA-5 and STA-6 Operations Plans. 

As explained above, since the concept of ‘stabilization’ is no longer valid, this was 

stricken. 

6. Specific Condition 28.E 

Item 6. The operational status of the STA, stating whether the STA is in Start-up, Stabilization or Routine 

Operations. If the facility is in Start-up Stabilization operations during the reporting period, the report shall also 

include the date at which the facility entered the Stabilization that Phase and the length of time it remained or is 

expected to remain in that phase; 

 Since the concept of ‘stabilization’ is no longer valid, this provision was stricken. 

 Information regarding start-up is needed since remedy milestone dates are in part, based 

 on that.