PROPOSED 

NUMERIC NUTRIENT CRITERIA 

FOR THE 

CHARLOTTE HARBOR NATIONAL ESTUARY PROGRAM 

ESTUARINE SYSTEM 

Prepared for: 

Charlotte Harbor National Estuary Program 

1926 Victoria Avenue 

Fort Myers, Florida 33901-3414 

Prepared by: 

Janicki Environmental, Inc. 

1155 Eden Isle Drive NE 

St. Petersburg, Florida 33704 

September 2011
2 

Table of Contents 

1.0 INTRODUCTION ............................................................................................................................. 3

2.0 OBJECTIVE ....................................................................................................................................... 6

3.0 DEVELOPMENT OF SEAGRASS, LIGHT ATTENUATION, AND CHLOROPHYLL A TARGETS ......... 6

3.2 DEVELOPMENT OF SEAGRASS TARGETS ............................................................................................... 7

3.3 DEVELOPMENT OF CHLOROPHYLL A TARGETS...................................................................................... 8

4.0 PROPOSED NUMERIC NUTRIENT CRITERIA ................................................................................ 10

5.0 IMPLEMENTATION ........................................................................................................................ 12

6.0 REFERENCES ................................................................................................................................... 13
3 

1.0 Introduction 

The Florida Department of Environmental Protection (FDEP) is currently developing a rule to 

establish numeric nutrient criteria for a number of water body types (FDEP website, 2011). The 

following summarizes the FDEP view on the development of numeric nutrient criteria in Florida. 

The overarching FDEP goal is to “manage nutrients in surface water (and groundwater) at loadings 

or concentrations that result in protection and maintenance of healthy, well-balanced aquatic 

communities”. Absent site-specific analyses, water quality criteria should be based on a 

quantifiable linkage between anthropogenic nutrient enrichment and a biological response (such as 

seagrass growth) that can be used to numerically interpret the narrative nutrient criteria. There is 

value in knowing whether nutrient concentrations are elevated to potentially environmentally 

harmful levels, but, conversely, it is equally important to identify adverse biological effects and 

determine if they are linked to nutrients before deciding that nutrient reduction strategies should be 

pursued. 

The Department recognizes the role of site-specific factors that affect nutrient responses and 

proposes to base new standards on establishing a systematic numeric interpretation of the existing 

narrative criteria. This concept is intended to implement Rule 62-302.530 (47)(b), FAC which 

states, “in 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.”

As envisioned by FDEP, the narrative nutrient criteria would continue to apply to all waterbodies, 

and numeric interpretations would be applied when adequate scientific information is available. 

The narrative would be implemented using a systematic structure that numerically interprets the 

narrative nutrient criteria for each waterbody in a hierarchical manner. 

Numeric interpretations are most accurate when determined as a site-specific function. Therefore, 

nutrient Total Maximum Daily Loads (TMDLs), Site Specific Alternative Criteria (SSAC), and other 

site specific actions written to achieve the narrative nutrient criteria should be given preference 

over more broadly applicable interpretations. 

The first tier of the hierarchical approach entails an evaluation of previously established site-specific 

numeric interpretations of the narrative criteria (including TMDLs, SSACs, and other interpretations 

embodied in an official Department action). This would be the primary interpretation of the 

narrative nutrient criteria. Currently, the Charlotte Harbor National Estuary Program (CHNEP) 

Policy Board has approved a series of segment-specific numeric nutrient criteria. FDEP is 

represented on the CHNEP Policy Board; therefore, the CHNEP estuarine area is presumably a 

candidate for inclusion in the first tier of the hierarchical approach. 

FDEP has also stated nutrient TMDLs may be expressed as concentrations or loads, and that loads 

do not have to be translated into concentrations to be deemed the numeric interpretation of the 

narrative nutrient criteria. This document presents concentration-based numeric nutrient criteria for 

the segments of the CHNEP. 

Finally, FDEP recognizes that future TMDL rules may include a response target (chlorophyll a, for 

example) designed to implement the narrative nutrient criterion. Currently, the recommended 
4 

assessment of the proposed numeric nutrient criteria for the CHNEP estuarine segments is built on 

assessing the achievement of a series of segment-specific chlorophyll a targets. 

Over the past several years, the CHNEP has conducted a series of tasks with the ultimate goal of

establishing estuarine numeric nutrient criteria for the CHNEP segments. This document 

summarizes these efforts. The first part of this document provides background information 

concerning the CHNEP estuarine system, including a brief physical characterization of the system 

and a summary of previous work completed with respect to CHNEP estuarine targets. The second 

part of this document provides the data and methodology utilized for developing estuarine numeric 

nutrient criteria for the CHNEP estuarine segments, the targets resulting from application of the 

methodology, the proposed numeric nutrient criteria, and the proposed methodology for 

implementation and compliance of the CHNEP estuarine numeric nutrient criteria. 

The Charlotte Harbor National Estuary Program Area and Its Watershed

The CHNEP area encompasses 11 interconnected estuaries and their watersheds in southwest 

Florida along the eastern Gulf of Mexico (Figure 1-1). The CHNEP watershed extends over 100 

miles from the river headwaters to the estuaries and includes 8 subwatersheds. The estuaries total 

over 284 square miles, which, for management purposes, are divided into 14 estuarine segments 

with distinctive resource management conditions. 

From north to south, the CHNEP estuarine complex stretches from Dona and Roberts Bay in 

Sarasota County, through Lemon Bay to the main body of Charlotte Harbor in Charlotte County, fed 

by the Tidal Myakka and Tidal Peace Rivers, to Pine Island Sound and Matlacha Pass in Lee 

County, joining San Carlos Bay which is fed by the Tidal Caloosahatchee River, and finally to 

Estero Bay. 

Charlotte Harbor is the largest and deepest of the estuaries, extending over 22 miles from river 

mouth to Gulf pass and reaching 20 feet deep in the harbor and over 70 feet deep at Boca Grande 

Pass. The smallest, shallowest bays are Dona and Roberts and Estero bays, which are, respectively, 

1 mile and 13 miles long and generally less than 6 feet deep. Lemon Bay is the narrowest estuary, 

about 3⁄4 of a mile wide. Pine Island Sound has the most extensive coverage of seagrasses (over 

26,000 acres) and Matlacha Pass is the tidal node between Charlotte Harbor and Caloosahatchee 

River waters. 

Circulation in the CHNEP is primarily driven by tidal exchange between the Gulf of Mexico and 

the freshwater inflows from three major rivers and numerous smaller tidal creeks. Dona and 

Roberts and Lemon bays are separated from the Gulf of Mexico by a series of barrier islands with 

passes at Venice Inlet, Stump Pass, and Gasparilla Pass. Freshwater inflows include three major 

rivers (Myakka, Peace, and Caloosahatchee rivers) and numerous smaller creeks. Daily exchange 

of water is greatest through Boca Grande Pass, which serves as the conduit between the Gulf of 

Mexico and Charlotte Harbor. Pine Island Sound has the most stable salinities due to passes at 

Boca Grande, Captiva, Redfish and San Carlos Bay, with little direct watershed inflow. Matlacha 

Pass has highly altered inflows from the urban areas of Cape Coral and Fort Myers and is connected 

indirectly to the Gulf in the south through San Carlos Bay. San Carlos Bay provides a direct 

connection between the Gulf of Mexico and the Caloosahatchee River. The Caloosahatchee River 

is a highly managed system that includes a series of locks between Lake Okeechobee and the lower 

portion of the Caloosahatchee River. Estero Bay has 3 moderate sized passes (Matanzas, Big 
5 

Carlos, and Little Carlos) and drains a relatively small but highly urbanized watershed through 

Hendry Creek, Mullock Creek, Spring Creek, Estero River, and Imperial River. 

Figure 1-1. Charlotte Harbor National Estuary Program segments. 
6 

2.0 Objective 

The objective of this document is to propose estuarine numeric nutrient criteria specific to the 

segments of the CHNEP: Dona and Roberts Bay, Upper Lemon Bay, Lower Lemon Bay, Tidal 

Myakka, Tidal Peace, Charlotte Harbor Proper (composed of East Wall, West Wall, Bokeelia, and 

Cape Haze), Matlacha Pass, Pine Island Sound, San Carlos Bay, Tidal Caloosahatchee, and Estero 

Bay. These segments were developed as part of a previous work order and are summarized in 

Janicki Environmental (2009a). These criteria are expressed as TN concentrations in these

segments. 

3.0 Development of Seagrass, Light Attenuation, and Chlorophyll 

a Targets 

This section provides a summary of work previously completed by the CHNEP in the establishment 

of segment-specific seagrass targets and their associated water quality targets. 

 

3.1 Background and Rationale

Charlotte Harbor was designated as an “estuary of national significance” and the CHNEP was 

established in 1995. CHNEP is a partnership of citizens, elected officials, resource managers and 

commercial and recreational resource users who are working together to improve the water quality 

and ecological integrity of the CHNEP’s diverse estuaries. A cooperative decision making process 

is used to address diverse resource management concerns throughout the 4,700 square mile 

watershed. 

CHNEP management actions are guided by the Comprehensive Conservation and Management 

Plan (CCMP), which identifies four priority problems including water quality degradation, 

hydrologic alterations, fish and wildlife habitat loss, and stewardship gaps. Fifteen quantifiable 

objectives and 64 priority actions have been established in order to effectively address the priority 

problems identified in the CCMP. While not explicitly stated, the CHNEP CCMP recognized the 

linkages between nutrient enrichment, algal productivity, light attenuation, and seagrass growth 

and reproduction in a similar fashion to the Tampa Bay Estuary Program nutrient loadingchlorophyll-seagrass paradigm. Technically sound, consensus based resource decisions are made 

through the CHNEP Management Conference which consists of the Technical Advisory, Citizens 

Advisory, Management and Policy Committees. 

Seagrass acreages throughout the CHNEP have been relatively stable since the 1950s but show 

significant spatial and temporal variability. Between 1950 and 1988, an estimated 5% of the 

seagrass acreage in the CHNEP was lost, with the highest losses in Pine Island Sound, Matlacha 

Pass and San Carlos Bay. Seagrass losses are attributed to physical alterations from dredge and fill 

activities, primarily the Intracoastal Waterway and Sanibel Causeway, and changes in freshwater 

inflows, especially in the major rivers. 

Seagrasses are used as a living resource basis for developing water quality targets for the CHNEP 

estuaries. Initial water quality targets were developed in 2005 based on seagrass light requirements 

at the maximum growth depth and the relationship of water clarity to key light attenuators: color 

dissolved organic matter (CDOM), chlorophyll a, and turbidity. Subsequently, beginning in 2009, 
7 

CHNEP began the process of refining the water quality targets based on updated light availability 

and water quality data based on seagrass acreage and a reference period approach (2003-2007). 

The refined water quality targets were developed and adopted by the CHNEP Management 

Conference through a series of tasks and reports, which include: validation of estuary segment 

scheme, seagrass targets, water clarity targets, nutrient loads, and total nitrogen (TN) and total 

phosphorus (TP) concentration and load targets. 

3.2 Development of Seagrass Targets 

One of the primary CHNEP goals is to maintain and/or restore seagrass coverage to its historic 

extent. The seagrass target project provided technically-defensible quantitative seagrass targets for 

the CHNEP ecosystem. Seagrass targets were developed and approved as a CHNEP management 

tool in August 2009 in order to track changes in an important ecological indicator over time (Janicki 

Environmental, 2009b). Establishment of seagrass targets provides a necessary basis for 

management decisions regarding water quality and other issues that can influence the distribution 

and persistence of this resource. Targets were defined through an analysis of historic and recent 

aerial surveys of the study area. 

The historic aerial photos used to establish the baseline extent of seagrass in the study area were 

dated circa 1950. Recent trends in and persistence of seagrass throughout the CHNEP were 

determined through analysis of GIS shapefiles based on aerial surveys executed biannually by the 

South and Southwest Florida Water Management Districts since 1988 (Appendix A provides time 

series plots of segment-specific seagrass acreages). Due to anthropogenic modifications in the 

estuary, such as shoreline build-out and the dredging of the Intracoastal Waterway (ICW), certain 

areas have been altered to the extent that they have no reasonable potential for restoration; these 

so-called non-restorable areas have been identified and removed from the analyses. 

The definition of the most appropriate seagrass targets was reached with input from the Technical 

Advisory Committee (TAC). The TAC recommended that targets be established as the greater of 

either the adjusted baseline acreage or the mean of all recent seagrass surveys (Janicki 

Environmental, 2009b). Application of this definition provided the targets identified for each 

harbor segment in Table 3-1.

In addition to defining these targets, an appropriate definition of a target range, i.e., the range of 

acceptable seagrass area, was also desired. The target range was defined as the range between the 

minimum and maximum areas from the recent seagrass surveys. The target range for each segment 

is also presented in Table 3-1.

Table 3-1. CHNEP Seagrass targets (from Janicki Environmental, 2009b). Unit of measure=acres.

Harbor Segment Adjusted 

Baseline

Mean Annual 

Extent 

(all years)

Protection 

Target

Restoration 

Target

Total 

Target Target Range

Dona and Roberts Bay* 112 91 91 21 112 70-124

Upper Lemon Bay 880 1,009 1,009 1,009 949-1,175

Lower Lemon Bay 2,882 2,502 2,502 380 2,882 2,396-2,597

Tidal Myakka River* 344 456 456 456 331-539

Tidal Peace River* 975 384 384 591 975 295-573
8 

Table 3-1. CHNEP Seagrass targets (from Janicki Environmental, 2009b). Unit of measure=acres.

Charlotte Harbor Proper

West Wall 2,106 1,907 1,907 199 2,106 1,676-2,121

East Wall 3,898 3,465 3,465 433 3,898 3,275-3,591

Cape Haze 5,670 6,998 6,998 6,998 6,709-7,464

Bokeelia 2,964 3,342 3,342 3,342 3,101-3,520

Pine Island Sound 23,757 26,837 26,837 26,837 25,941-29,204

Matlacha Pass 9,315 7,582 7,582 1,733 9,315 6,055-7,619

Tidal Caloosahatchee 

River* 93 87 87 6 93 2-103

San Carlos Bay 3,118 4,372 4,372 4,372 3,709-5,376

Estero Bay 3,662 3,071 3,071 591 3,662 2,393-3,409

* These riverine segments may have underreported seagrass acreages, due to difficulty in delineating 

seagrass in highly colored waters. These numbers are presented for completeness only and should not 

be used for reporting of seagrass loss or gain over time. 

3.3 Development of Chlorophyll a Targets 

Establishment of defensible, protective environmental endpoints largely depends upon the 

definition of a defensible baseline. CHNEP considered three candidate methods for defining 

chlorophyll a thresholds (Janicki Environmental, 2011a). These methods were: 

 Regulatory-based Method, 

 Optical Model Method, and 

 Reference Period Method. 

Seagrass and water clarity targets have been established for the segments of the CHNEP area. 

Given that the recent extents of seagrasses in some segments are meeting their established targets, it 

logically follows that recent water clarity and chlorophyll a concentrations are protective of the 

seagrasses in those segments that are meeting established targets. It was determined that the 

reference period approach was most appropriate for target setting. However, for the segments that 

are not meeting their targets, the same assumption is not valid. This was considered when 

developing chlorophyll a targets for the system utilizing the reference period approach. A 

description of the data used for target development is provided in Appendix A. 

The Tampa Bay Estuary Program (TBEP) (Janicki and Wade, 1996) and Sarasota Bay Estuary 

Program (SBEP) (Janicki Environmental, 2010c) used a similar reference period approach to define 

chlorophyll a targets. Both programs recognized that there may be years in which chlorophyll a

targets may be exceeded without causing significant reductions in seagrass cover. Therefore, there 

is some allowable amount of variation that should not elicit a significant degradation in water 

quality and therefore seagrass coverage. The SBEP defined this level of variation as the standard 

deviation around the mean annual chlorophyll a concentrations in each segment for the entire 

period of record. The target was defined as the annual mean of the reference period, i.e., the 

period that was deemed to be protective on seagrass and water clarity. Therefore, a distinction is 

made between a target, i.e., a desired chlorophyll a concentration and a threshold, i.e., a 

chlorophyll a concentration above which undesirable chlorophyll a concentrations exist. 
9 

Given the experience of the neighboring estuary programs, the CHNEP TAC decided to use a 

similar approach, but with different thresholds depending on whether or not a segment was 

classified as “restoration” or “protection” for seagrass. If a segment is classified as “protection”, it 

logically follows that water clarity and chlorophyll a concentrations are protective of seagrasses. 

Therefore, the chlorophyll a threshold for segments that are classified as “protection” is calculated 

by summing the mean plus one standard deviation. This is the same strategy that was employed by 

the SBEP in criteria development for the SBEP segments. However, if the segment is under 

“restoration”, the chlorophyll target is calculated by summing the mean plus one-half standard 

deviation. This provides a threshold that is more stringent than for segments that are classified as 

“protection” because the “restoration” segments have not achieved the desired levels of seagrass 

coverage. The reference period used to establish the chlorophyll a targets was 2003-2007. This 

corresponds to the time period used in establishing the water clarity targets for CHNEP (Janicki 

Environmental, 2010a). The mean chlorophyll a concentrations for the reference period (targets), 

along with the standard deviation (for the period of record) and the thresholds are presented for 

each segment in Table 3-2. 

Table 3-2. Recommended chlorophyll a targets and thresholds (μg/L) developed based on reference 

period (2003-2007).

Segment Restoration/

Protection

Target

Chlorophyll a 

(μg/L)

Standard Deviation 

of Annual Means

(μg/L)

Threshold 

Chlorophyll a

(μg/L)

Dona and Roberts Bays Restoration 4.3 1.2 4.9

Upper Lemon Bay Protection 6.7 2.2 8.9

Lower Lemon Bay Restoration 5.1 2.0 6.1

Tidal Myakka Protection 8.9 2.8 11.7

Tidal Peace Restoration 10.6 4.0 12.6

Charlotte Harbor Proper 

(EW+WW+BK+CH)

Restoration/ 

Protection 4.9 2.4 7.3/6.1

Matlacha Pass Restoration 4.0 4.1 6.1

Pine Island Sound Protection 5.1 1.4 6.5

San Carlos Bay Protection 2.8 0.7 3.5

Tidal Caloosahatchee Restoration 9.0 n/a 6.9 (TMDL)

Estero Bay Restoration 4.9 2.0 5.9

Since establishing seagrass targets for tidal rivers is questionable due to issues with color and 

visibility (Janicki Environmental, 2009b), the chlorophyll thresholds for the Tidal Myakka, Tidal 

Peace, and Tidal Caloosahatchee rivers were not used in criteria development. Instead, the 

chlorophyll targets for the downstream areas, Charlotte Harbor Proper for the Tidal Peace and Tidal 

Myakka and San Carlos Bay for Tidal Caloosahatchee, were used. Please note that a proposed 

Total Maximum Daily Load (TMDL) has been developed for the Tidal Caloosahatchee River as a 

result of the system being identified as impaired. In the proposed TMDL, a target chlorophyll a

concentration of 6.9 μg/L was identified for the Tidal Caloosahatchee. 
10

4.0 Proposed Numeric Nutrient Criteria 

The CHNEP employed evaluation of stressor-response relationships in a similar manner to that 

proposed by Janicki Environmental (2010b) and EPA (2010). This approach involves the 

development of a quantitative relationship (i.e., model) between chlorophyll a and some measure 

of nutrient condition. In this case, the independent variables used in the model-building process 

included loadings, concentrations, and estimates of residence time. The loadings data (Janicki 

Environmental, 2010d) included monthly hydrologic, TN, and TP loads as well as cumulative total 

loads extending from two to six months (e.g., 2-month cumulative TN load = TN load current 

month + TN load one- month prior). The water quality constituents included TN and TP 

concentrations along with numerous other constituents. 

A flowchart of the overall process used to develop numeric nutrient criteria for the segments of the 

CHNEP area is presented in Figure 4-1. Following this flowchart, numeric nutrient criteria in terms 

of TN concentrations were developed for each segment. 

Figure 4-1. Flowchart of Process Used to Develop Numeric Nutrient Criteria. 

A complete presentation of the process followed to develop the proposed criteria for CHNEP can 

be found in Janicki Environmental (2011a). A description of the data utilized is provided in 

Appendix A. 
11

The CHNEP Management and Policy committees approved the TAC recommendations for the TN 

concentration-based numeric criteria (Table 4-1) based on the Reference Period approach, as no 

appropriate stressor-response relationships were found that could be used to develop defensible 

numeric nutrient criteria. For further description of the numeric nutrient criteria development and 

comparison to observed conditions, see Janicki Environmental (2011a) and Appendix B. 

Table 4-1. Recommended numeric nutrient criteria based on the 

reference period approach for TN concentration.

Segment Candidate Criterion

Dona and Roberts Bays 0.42 mg/L

Upper Lemon Bay 0.56 mg/L

Lower Lemon Bay 0.62 mg/L

Tidal Myakka 1.02 mg/L

Tidal Peace 1.08 mg/L

Charlotte Harbor Proper 0.67 mg/L

Matlacha Pass 0.58 mg/L

Pine Island Sound 0.57 mg/L

Tidal Caloosahatchee TBD

San Carlos Bay 0.56 mg/L

Estero Bay 0.63 mg/L

Additionally, criteria were developed in terms of TP concentration and TN and TP loads (Janicki 

Environmental, 2011b), based on the reference period approach as for TN concentrations. These 

criteria are provided in Table 4-2 for use if needed. Description of the derivation of these 

alternative criteria and comparison to observed conditions are provided in Appendix B. 

Table 4-2. Alternative numeric nutrient criteria expressed as TP concentrations and TN and TP 

loads derived using the Reference Period Approach. The reference period was 2003-2007.

Segment TP Concentration

(mg/L)

TN Load

(tons/yr)

TP Load

(tons/yr)

Dona and Roberts Bay 0.18 250 48

Upper Lemon Bay 0.26 102 18

Lower Lemon Bay 0.17 136 21

Charlotte Harbor Proper1 0.19 5,987 2,281

Pine Island Sound 0.06 190 8

San Carlos Bay 0.07 TBD TBD

Tidal Myakka River 0.31 1,407 351

Tidal Peace River 0.50 4,343 1,960

Matlacha Pass 0.08 216 24

Tidal Caloosahatchee River TBD TBD TBD

Estero Bay 0.07 587 61

1

Loads are sum of Charlotte Harbor Proper and the Tidal Peace and Myakka Rivers. 
12

5.0 Implementation 

The proposed compliance assessment strategy involves two steps. The initial step is the 

comparison of the mean annual chlorophyll a concentrations in each bay segment to the 

established chlorophyll a thresholds. Compliance is achieved if the threshold is met in that year. If 

the chlorophyll a threshold is exceeded in more than two years during any five-year period, the 

second step would be an assessment of nitrogen concentrations during that period. The 

justification for this “2-in-5 year” compliance assessment has been developed (Janicki 

Environmental, 2011c) and summarized in Appendix C. 

The recommendation for compliance assessment also hinges on the availability of the appropriate 

data for a defensible assessment. Thus, how the specific spatial and temporal averaging has been 

conducted in the development of the targets and thresholds as well as the compliance assessment is 

critical. The following discusses this aspect of the implementation of the proposed numeric 

nutrient criteria for the CHNEP estuarine segments. 

From the initial efforts to establish defensible water quality targets, ambient water quality data have 

been obtained from the following agencies and programs: 

 Southwest Florida Water Management District, 

 South Florida Water Management District, 

 Sarasota County, 

 Lee County, 

 Peace River Manasota Regional Water Supply Authority, 

 Coastal Charlotte Harbor Monitoring Network, 

 Charlotte Harbor Volunteer Monitoring Network, 

 Charlotte Harbor Aquatic Preserves, 

 City of Cape Coral, and 

 Florida International University. 

Maps showing the locations of these sites are presented in Appendix D. 

Defensible compliance assessment will depend upon continued monitoring to ensure that the 

annual assessment can be completed for attainment of the proposed chlorophyll a thresholds and 

TN criteria. Consideration must also be given to the temporal averaging. The mean annual 

chlorophyll a concentrations have been calculated by first calculating the segment-specific 

arithmetic monthly means and subsequently calculating an arithmetic annual mean. The 

compliance would be assessed by calculating the chlorophyll a threshold i.e., the sum of the 

arithmetic annual mean and the estimate of the interannual variability (see Table 3-2). The TN 

compliance would be based on the arithmetic annual mean for each bay segment, with the 

concentration criteria as provided in Table 4-1. 
13

6.0 References 

Florida Department of Environmental Protection (FDEP) website. 2011. 

http://www.dep.state.fl.us/water/wqssp/nutrients/index.htm

Janicki, A.J. and D.L. Wade. 1996. Estimating critical nitrogen loads for the Tampa Bay estuary: an 

empirically based approach to setting management targets. Technical Publication 06-96 of the 

Tampa Bay National Estuary Program. Prepared by Coastal Environmental, Inc. 

Janicki Environmental. 2009a. Water Quality Targets Refinement Project Task 1: Harbor 

Segmentation Scheme Interim Report 1. Prepared for Charlotte Harbor National Estuary Program, 

Ft. Myers, FL. 

Janicki Environmental, Inc. 2009b. Water Quality Target Refinement Project – Task 2: Seagrass 

target development. Interim Report 2. Prepared for Charlotte Harbor National Estuary Program, Ft. 

Myers, FL. Authors: Janicki, A., M. Dema, and M. Wessel 

Janicki Environmental, Inc. 2010a. Water Quality Target Refinement Project, Task 3: Water 

Clarity Target Development. Interim Report 3. Prepared for Charlotte Harbor National Estuary 

Program. Ft. Myers, FL. 

Janicki Environmental, Inc. 2010b. Empirical Approaches to Establishing Numeric Nutrient 

Criteria for Southwest Florida Estuaries. Prepared for Tampa Bay Estuary Program, Sarasota Bay 

Estuary Program, and Charlotte Harbor National Estuary Program. 

Janicki Environmental, Inc. 2010c. Recommended Numeric Nutrient Criteria for Sarasota Bay. 

Prepared for Sarasota Bay Estuary Program. Sarasota, FL. 

Janicki Environmental, Inc. 2010d. Water Quality Target Refinement Project, Task 4: Pollutant 

Loading Estimates Development, Interim Report 4. Prepared for Charlotte Harbor National Estuary 

Program. Ft. Myers, FL. 

Janicki Environmental, Inc. 2011a. Development of Numeric Nutrient Criteria for the Estuarine 

Waters of the Charlotte Harbor National Estuary Program. Task 7: Numeric Nutrient Criteria 

Development. Interim Report 6. Prepared for Charlotte Harbor National Estuary Program, Fort 

Myers, FL. 

Janicki Environmental, Inc. 2011b. Development of Numeric Nutrient Criteria for the Estuarine 

Waters of the Charlotte Harbor National Estuary Program. Task 8 - TN and TP Loading and 

Concentration-Based Criteria. Interim Report 6. Prepared for Charlotte Harbor National Estuary 

Program, Fort Myers, FL. 

Janicki Environmental, Inc. 2011c. Charlotte Harbor Numeric Nutrient Criteria: Task 9 - 

Implementation Issues. Interim Report 6. Prepared for Charlotte Harbor Estuary Program. Ft. 

Myers, FL. 
14

U.S. Environmental Protection Agency (EPA). 2010. Methods and Approaches for Deriving 

Numeric Criteria for Nitrogen/Phosphorus Pollution in Florida’s Estuaries, Coastal Waters, and 

Southern Inland Flowing Waters. 
A-1

APPENDIX A. 

Data Description and 

Assessment of Seagrass, Water Quality, and Loadings 

1.0 Data Description 

This appendix provides identification and description of the seagrass, water quality, and loadings 

data utilized for establishing numeric nutrient criteria in the Charlotte Harbor National Estuary 

Program estuarine system. 

1.1 Seagrasses

Seagrass targets were developed and approved as a CHNEP management tool in August 2009 in 

order to track changes in an important ecological indicator over time (Janicki Environmental, 2009). 

Baseline seagrass coverage was determined through photo-interpretation of aerial photos of the 

study area from circa 1950 obtained from the National Archives in Washington, DC. The CHNEP 

contracted Photo Science, experts in photo-interpretation services, which provided electronic data 

coverage of the area of interest for the CHNEP using ArcGIS9. This coverage served as a historic 

baseline from which to compare recent surveys conducted by the South and Southwest Florida 

Water Management Districts (Janicki Environmental, 2009). Historic (1950) and recent (1988 to 

present) surveyed seagrass acreages were compared to establish seagrass targets. These seagrass 

targets were designed to maintain and/or restore seagrass acreage to its historical extent. While the 

extent of seagrass in the CHNEP area may be governed by a variety of processes including erosion, 

salinity changes, biological perturbations, prop scarring and sedimentation, water clarity is thought 

to be the principal controlling factor in the long-term health of seagrasses in the study area. 

Therefore, management-level water clarity targets that are related to the light requirements of 

seagrass were developed to allow managers to correlate changes in water clarity conditions and 

seagrass conditions over time. 

The CHNEP seagrass target for each harbor segment is the greater of either the adjusted baseline 

acreage or the mean of all recent seagrass surveys (Janicki Environmental, 2009). Application of 

this definition provided the targets identified for each harbor segment in Table 1-1.
A-2

Table 1-1. CHNEP Seagrass targets (from Janicki Environmental, Inc., 2009). Unit of measure=acres.

Harbor Segment Adjusted 

Baseline

Mean Annual 

Extent 

(all years)

Protection 

Target

Restoration 

Target

Total 

Target

Target Range

Dona and Roberts Bay* 112 91 91 21 112 70-124

Upper Lemon Bay 880 1,009 1,009 1,009 949-1,175

Lower Lemon Bay 2,882 2,502 2,502 380 2,882 2,396-2,597

Tidal Myakka River* 344 456 456 456 331-539

Tidal Peace River* 975 384 384 591 975 295-573

West Wall 2,106 1,907 1,907 199 2,106 1,676-2,121

East Wall 3,898 3,465 3,465 433 3,898 3,275-3,591

Cape Haze 5,670 6,998 6,998 6,998 6,709-7,464

Bokeelia 2,964 3,342 3,342 3,342 3,101-3,520

Pine Island Sound 23,757 26,837 26,837 26,837 25,941-29,204

Matlacha Pass 9,315 7,582 7,582 1,733 9,315 6,055-7,619

Tidal Caloosahatchee 

River* 93 87 87 6 93 2-103

San Carlos Bay 3,118 4,372 4,372 4,372 3,709-5,376

Estero Bay 3,662 3,071 3,071 591 3,662 2,393-3,409

Total 59,776 62,103 62,103 3,954 66,057 56,902-67,415

* These riverine segments may have underreported seagrass acreages, due to difficulty in delineating 

seagrass in highly colored waters. These numbers are presented for completeness only and should not 

be used for reporting of seagrass loss or gain over time. 

1.2 Water Quality and Loadings 

A number of data sources were used to develop the data base used to determine numeric nutrient 

criteria for the estuarine waters of the CHNEP. These included ambient water quality data, 

hydrologic and nutrient loading estimates, seagrass coverage, and bathymetry. These data sources 

are described in the following subsections. 

Ambient water quality data were obtained from the following agencies and programs: 

 Southwest Florida Water Management District, 

 South Florida Water Management District, 

 Sarasota County, 

 Lee County, 

 Peace River Manasota Regional Water Supply Authority, 

 Coastal Charlotte Harbor Monitoring Network, 

 Charlotte Harbor Volunteer Monitoring Network, 

 Charlotte Harbor Aquatic Preserves, 

 City of Cape Coral, and 

 Florida International University. 
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Estimates of hydrologic, TN, and TP loadings have recently been developed for Charlotte Harbor 

(Janicki Environmental, 2010). The loading sources include: 

 atmospheric deposition directly to the surface of the estuary, 

 nonpoint sources, 

 septic tanks (on-site sewage treatment and disposal systems), and 

 domestic and industrial point sources (wastewater treatment facilities and industrial facility 

discharges). 

Monthly loading estimates for each CHNEP segment are reported. 

2.0 Assessment of Conditions 

The following sections provide segment-specific comparisons of observed conditions to the 

seagrass targets, and summaries of TN, TP, and chlorophyll a concentrations and hydrologic, TN, 

and TP loadings for each CHNEP. Times series of monthly mean values for each bay segment were 

produced to allow visual inspection of trends over time and to allow a comparison between bay 

segments. 

2.1 Seagrass

The following provides the segment-specific seagrass targets, and acreage estimates in Figures 2-1 

through 2-8. The riverine segments (Dona and Roberts Bay, Tidal Myakka, Tidal Peace and Tidal 

Caloosahatchee) may have underreported seagrass acreages, due to difficulty in delineating seagrass 

in highly colored waters. 

 Dona and Roberts Bay (Figure 2-1)

- The seagrass target for this segment is 112 acres (Janicki Environmental, 2009). 

- Dona and Roberts Bay is classified as a seagrass “restoration” segment.

 Upper and Lower Lemon Bay (Figure 2-2)

- The seagrass targets are 1,009 acres for Upper Lemon Bay and 2,882 acres for Lower 

Lemon Bay (Lemon Bay total = 3,891) (Janicki Environmental, 2009). 

- Upper Lemon Bay is classified as a seagrass “protection” segment, while Lower Lemon Bay 

is classified as a seagrass “restoration” segment.

 Charlotte Harbor Proper (Figure 2-3)

- The seagrass target is 16,344 acres (West Wall=2,106 acres, East Wall=3,898 acres, Cape 

Haze=6,998, Bokeelia=3,342 acres) (Janicki Environmental, 2009). 

- Cape Haze and Bokeelia are classified as seagrass “protection” segments, while West Wall 

and East Wall are classified as seagrass “restoration” segments. In order to be conservative, 

Charlotte Harbor Proper was classified as seagrass “restoration.

 Tidal Myakka (Figure 2-4)

- The seagrass target for this segment is 456 acres (Janicki Environmental, 2009). 

- Tidal Myakka is classified as a seagrass “protection” segment.
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 Tidal Peace (Figure 2-5)

- The seagrass target for this segment is 975 acres (Janicki Environmental, 2009). 

- Tidal Peace is classified as a seagrass “restoration” segment.

 Pine Island Sound and Matlacha Pass (Figure 2-6)

- The seagrass targets are 26,837 acres for Pine Island Sound and 9,315 acres for Matlacha 

Pass (Janicki Environmental, 2009). 

- Pine Island Sound is classified as a seagrass “protection” segment, while Matlacha Pass is 

classified as a seagrass “restoration” segment.

 San Carlos Bay (Figure 2-7) and Tidal Caloosahatchee 

- The seagrass targets are 4,372 acres for San Carlos Bay and 93 acres for Tidal 

Caloosahatchee (Janicki Environmental, 2009). 

- San Carlos Bay is classified as a seagrass “protection” segment, while Tidal Caloosahatchee 

is classified as a seagrass “restoration” segment.

 Estero Bay (Figure 2-8)

- The seagrass target for this segment is 3,662 acres (Janicki Environmental, 2009). 

- Estero Bay is classified as a seagrass “restoration” segment.

Figure 2-1. Annual seagrass acreages in Dona and Roberts Bays (target range = 70-124 acres). 

0

20

40

60

80

100

120

140

1988 1994 1999 2001 2004 2006 2008

Seagrass Coverage (acres)
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Figure 2-2. Annual seagrass acreages in Upper and Lower Lemon Bay (target range = 3,345-3,772 acres).

Figure 2-3. Annual seagrass acreages in Charlotte Harbor Proper (target range = 14,761-16,696 acres). 

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

18,000

1988 1994 1999 2001 2004 2006 2008

West Wall East Wall Cape Haze Bokeelia

Seagrass 
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Figure 2-4. Annual seagrass acreages in Tidal Myakka (target range = 331-539 acres). 

Figure 2-5. Annual seagrass acreages in Tidal Peace (target range = 295-573 acres). 

0

100

200

300

400

500

600

1988 1994 1999 2001 2004 2006 2008

Seagrass 
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Figure 2-6. Annual seagrass acreages in Pine Island Sound and Matlacha Pass (target range = 36,152-

36,823 acres). 

Figure 2-7. Annual seagrass acreages in San Carlos Bay (target range = 3,709-5,376 acres). 

0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

1999 2003 2004 2006 2008

0

5,000

10,000

15,000

20,000

25,000

30,000

35,000

40,000

1999 2003 2004 2006 2008

Pine Island Sound Matlacha Pass

Seagrass Coverage (acres)
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Figure 2-8. Annual seagrass acreages in Estero Bay (target range = 2,393-3,409 acres). 

2.2 Total Nitrogen Concentrations 

Times series of monthly mean values for each segment were produced to allow visual inspection of 

trends over time and to allow a comparison between bay segments. Time series plots of monthly 

TN concentrations are provided for each segment in Figures 2-9 through 2-18. 

0

500

1,000

1,500

2,000

2,500

3,000

3,500

4,000

1999 2003 2004 2006 2008

Seagrass Coverage (acres)
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Figure 2-9. Monthly TN concentrations (mg/L) in Dona and Roberts Bays. 

Figure 2-10. Monthly TN concentrations (mg/L) in Upper and Lower Lemon Bay. 
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Figure 2-11. Monthly TN concentrations (mg/L) in Charlotte Harbor Proper. 

Figure 2-12. Monthly TN concentrations (mg/L) in Tidal Myakka. 
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Figure 2-13. Monthly TN concentrations (mg/L) in Tidal Peace. 

Figure 2-14. Monthly TN concentrations (mg/L) in Pine Island Sound. 
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Figure 2-15. Monthly TN concentrations (mg/L) in Matlacha Pass. 

Figure 2-16. Monthly TN concentrations (mg/L) in San Carlos Bay. 
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Figure 2-17. Monthly TN concentrations (mg/L) in Tidal Caloosahatchee. 

Figure 2-18. Monthly TN concentrations (mg/L) in Estero Bay. 
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2.3 Total Phosphorus Concentrations 

As for TN concentrations, times series of monthly mean TP values for each segment were produced 

to allow visual inspection of trends over time and to allow a comparison between bay segments. 

Time series plots of monthly TP concentrations are provided for each segment in Figures 2-19 

through 2-28.

Figure 2-19. Monthly TP concentrations (mg/L) in Dona and Roberts Bays. 
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Figure 2-20. Monthly TP concentrations (mg/L) in Upper and Lower Lemon Bay. 

Figure 2-21. Monthly TP concentrations (mg/L) in Charlotte Harbor Proper. 
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Figure 2-22. Monthly TP concentrations (mg/L) in Tidal Myakka. 

Figure 2-23. Monthly TP concentrations (mg/L) in Tidal Peace. 
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Figure 2-24. Monthly TP concentrations (mg/L) in Pine Island Sound. 

Figure 2-25. Monthly TP concentrations (mg/L) in Matlacha Pass. 
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Figure 2-26. Monthly TP concentrations (mg/L) in San Carlos Bay. 

Figure 2-27. Monthly TP concentrations (mg/L) in Tidal Caloosahatchee. 
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Figure 2-28. Monthly TP concentrations (mg/L) in Estero Bay. 

2.4 Chlorophyll a

As for nutrient concentrations, times series of monthly mean chlorophyll a values for each segment 

were produced to allow visual inspection of trends over time and to allow a comparison between 

bay segments. Time series plots of monthly chlorophyll a concentrations are provided for each 

segment in Figures 2-29 through 2-38.
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Figure 2-29. Monthly chlorophyll a concentrations (μg/L) in Dona and Roberts Bays. 

Figure 2-30. Monthly chlorophyll a concentrations (μg/L) in Upper and Lower Lemon Bay. 
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Figure 2-31. Monthly chlorophyll a concentrations (μg/L) in Charlotte Harbor Proper. 

Figure 2-32. Monthly chlorophyll a concentrations (μg/L) in Tidal Myakka. 
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Figure 2-33. Monthly chlorophyll a concentrations (μg/L) in Tidal Peace. 

Figure 2-34. Monthly chlorophyll a concentrations (μg/L) in Pine Island Sound. 
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Figure 2-35. Monthly chlorophyll a concentrations (μg/L) in Matlacha Pass. 

Figure 2-36. Monthly chlorophyll a concentrations (μg/L) in San Carlos Bay. 
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Figure 2-37. Monthly chlorophyll a concentrations (μg/L) in Tidal Caloosahatchee. 

Figure 2-38. Monthly chlorophyll a concentrations (μg/L) in Estero Bay. 
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2.5 Hydrologic, Total Nitrogen, and Total Phosphorus Loadings 

Hydrologic and nutrient loads were estimated for the period 1995-2007 for the segments of the 

CHNEP area. The total annual hydrologic, TN, and TP loads to each bay segment are presented in 

Figures 2-39 through 2-48. 

Figure 2-39. Time series of TN loads (top plot), TP loads (middle plot), and hydrologic loads (bottom plot) 

for Dona and Roberts Bays. 
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Figure 2-40. Time series of TN loads (top plot), TP loads (middle plot), and hydrologic loads (bottom plot) 

for Lemon Bay. 
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Figure 2-41. Time series of TN loads (top plot), TP loads (middle plot), and hydrologic loads (bottom plot) 

for Charlotte Harbor Proper. 
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Figure 2-42. Time series of TN loads (top plot), TP loads (middle plot), and hydrologic loads (bottom plot) 

for Tidal Myakka. 
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Figure 2-43. Time series of TN loads (top plot), TP loads (middle plot), and hydrologic loads (bottom plot) 

for Tidal Peace. 
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Figure 2-44. Time series of TN loads (top plot), TP loads (middle plot), and hydrologic loads (bottom plot) 

for Pine Island Sound. 
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Figure 2-45. Time series of TN loads (top plot), TP loads (middle plot), and hydrologic loads (bottom plot) 

for Matlacha Pass. 
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Figure 2-46. Time series of TN loads (top plot), TP loads (middle plot), and hydrologic loads (bottom plot) 

for San Carlos Bay. 
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Figure 2-47. Time series of TN loads (top plot), TP loads (middle plot), and hydrologic loads (bottom plot) 

for Tidal Caloosahatchee. 
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Figure 2-48. Time series of TN loads (top plot), TP loads (middle plot), and hydrologic loads (bottom plot) 

for Estero Bay. 
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3.0 References 

Janicki Environmental, Inc. 2009. Water Quality Target Refinement Project – Task 2: Seagrass 

target development. Interim Report 2. Prepared for Charlotte Harbor National Estuary Program, Ft. 

Myers, FL. Authors: Janicki, A., M. Dema, and M. Wessel. 

Janicki Environmental, Inc. 2010. Water Quality Target Refinement Project, Task 4: Pollutant 

Loading Estimates Development, Interim Report 4. Prepared for Charlotte Harbor National Estuary 

Program. Ft. Myers, FL. 
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APPENDIX B. 

Criteria Expressed as TN and TP Concentrations, and as 

TN and TP Loads 

1.0 Introduction 

This appendix provides summaries of the derivation and application of the recommended numeric 

nutrient criteria for the CHNEP. Segment-specific stressor-response relationships between 

chlorophyll a and nitrogen concentrations were developed, but left a considerable amount of 

variability unexplained. Therefore, the Policy Committee agreed to develop TN concentration 

criteria based on the reference period approach. The same approach was utilized for developing 

criteria in terms of TP concentrations and TN and TP loads, should these be necessary. 

2.0 Total Nitrogen Concentrations 

The CHNEP has developed recommended numeric nutrient criteria as segment-specific mean 

annual total nitrogen concentrations (Janicki Environmental, 2011a). The strategy for developing 

the numeric nutrient criteria is based on the chlorophyll a thresholds (Table 2-1) (Janicki 

Environmental, 2011a). The following describes the approach used. 

Table 2-1. Recommended chlorophyll a targets and thresholds (μg/L) developed based on 

reference period (2003-2007).

Segment Restoration/

Protection

Target

Chlorophyll a 

(μg/L)

Standard Deviation 

of Annual Means

(μg/L)

Threshold 

Chlorophyll a

(μg/L)

Dona and Roberts Bays Restoration 4.3 1.2 4.9

Upper Lemon Bay Protection 6.7 2.2 8.9

Lower Lemon Bay Restoration 5.1 2.0 6.1

Tidal Myakka Protection 8.9 2.8 11.7

Tidal Peace Restoration 10.6 4.0 12.6

Charlotte Harbor Proper 

(EW+WW+BK+CH)

Restoration/ 

Protection 4.9 2.4 7.3/6.1

Matlacha Pass Restoration 4.0 4.1 6.1

Pine Island Sound Protection 5.1 1.4 6.5

San Carlos Bay Protection 2.8 0.7 3.5

Tidal Caloosahatchee Restoration 9.0 n/a 6.9 (TMDL)

Estero Bay Restoration 4.9 2.0 5.9

A data analysis plan developed previously by Janicki Environmental (2010) identified a series of 

techniques that could be used to estimate statistically defensible relationships between chlorophyll 

a concentrations and nutrient concentrations and/or loadings, including linear regression, logistic 
B-2

regression, and change point analysis. A flowchart of the overall process used to develop numeric 

criteria for the segments of the CHNEP area is presented in Figure 2-1. Following this flowchart, 

numeric nutrient criteria in terms of TN concentrations were developed for each segment. 

Figure 2-1. Flowchart of Process Used to Develop Numeric Nutrient Criteria. 

2.1 Dona and Roberts Bays 

While a statistically significant relationship was identified between chlorophyll a and TN 

concentration for Dona and Roberts Bays, a considerable amount of variability was left unexplained 

by this relationship. Based on discussions with the CHNEP Technical Advisory Committee, there is 

not sufficient confidence in the use of this regression to develop defensible numeric nutrient 

criterion due to the amount of variability left unexplained by the regression. Therefore, as 

described in Figure 2-1, the reference period approach was recommended for developing a TN 

concentration criterion for Dona and Roberts Bays. As Dona and Roberts Bays is classified as a 

seagrass “restoration” segment, the TN concentration criterion is calculated by summing the annual 

mean from the reference period (2003-2007) plus 1⁄2 standard deviation (for the period of record). 

This results in the following TN concentration criterion for Dona and Roberts Bays: 

TN criterion = 0.40 mg/l (mean) + 1⁄2 * 0.04 (SD) = 0.42 mg/l 
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A comparison of the candidate numeric TN concentration criterion based on the Reference Period 

method is presented in Figure 2-2. 

Figure 2-2. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in Dona and Roberts Bays. 

2.2 Lemon Bay 

Lemon Bay has been divided into the Upper and Lower Lemon Bay segments for previous work 

performed by the CHNEP (Janicki Environmental, 2009). Because the reference period divided 

Lemon Bay into Upper and Lower Lemon Bay segments and light and seagrass targets were 

developed individually for Upper and Lower Lemon Bay, an attempt was made to develop numeric 

nutrient criteria that are specific to the Upper and Lower Lemon Bay segments. 

Based on discussions with the CHNEP Technical Advisory Committee, there is not sufficient 

confidence in the Upper Lemon Bay regression to develop defensible numeric nutrient criterion 

due to the amount of variability left unexplained by the regression. Therefore, as described in 

Figure 2-1, the reference period approach was recommended for developing TN concentration 

criteria for Upper and Lower Lemon bays. As Upper Lemon Bay is classified as “protection” for 

seagrass, the TN concentration criterion is calculated by summing the annual mean from the 

reference period (2003-2007) plus one standard deviation (for the period of record): 

 

TN criterion = 0.52 mg/l (mean) + 0.04 (SD) = 0.56 mg/l 
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Lower Lemon Bay is classified as a seagrass “restoration” segment, therefore the TN concentration 

criterion is calculated by summing the annual mean from the reference period (2003-2007) plus 1⁄2 

standard deviation (for the period of record): 

TN criterion = 0.56 mg/l (mean) + 1⁄2 * 0.12 (SD) = 0.62 mg/l 

A comparison of the candidate numeric TN concentration criteria for Upper and Lower Lemon bays 

based on the Reference Period method are presented in Figure 2-3 and Figure 2-4, respectively.

Figure 2-3. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in Upper Lemon Bay. 
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Figure 2-4. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in Lower Lemon Bay. 

2.3 Charlotte Harbor Proper 

Based on discussions with the CHNEP Technical Advisory Committee, there is not sufficient 

confidence in the Charlotte Harbor Proper regression or changepoint analysis to develop a 

defensible numeric nutrient criterion. Therefore, as described in Figure 2-1, the reference period 

approach was recommended for developing a TN concentration criterion for Charlotte Harbor 

Proper. As Charlotte Harbor Proper is classified as “restoration” for seagrass, the TN concentration 

criterion is calculated by summing the annual mean from the reference period (2003-2007) plus 1⁄2 

standard deviation (for the period of record): 

 

TN criterion = 0.60 mg/l (mean) + 1⁄2 * 0.14 (SD) = 0.67 mg/l 

A comparison of the candidate numeric TN concentration criteria for Charlotte Harbor Proper 

based on the Reference Period method is presented in Figure 2-5. 
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Figure 2-5. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in Charlotte Harbor Proper. 

2.4 Tidal Myakka 

Based on discussions with the CHNEP Technical Advisory Committee, there is not sufficient 

confidence in the Tidal Myakka changepoint analysis to develop a defensible numeric nutrient 

criterion. Therefore, as described in Figure 2-1, the reference period approach was recommended 

for developing a TN concentration criterion for Tidal Myakka. As the segment is classified as 

“protection” for seagrass, the TN concentration criterion is calculated by summing the annual mean 

from the reference period (2003-2007) plus one standard deviation (for the period of record): 

 

TN criterion = 0.95 mg/l (mean) + 0.07 (SD) = 1.02 mg/l 

A comparison of the candidate numeric TN concentration criteria for Tidal Myakka based on the 

Reference Period method is presented in Figure 2-6.
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Figure 2-6. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in Tidal Myakka. 

2.5 Tidal Peace 

Based on discussions with the CHNEP Technical Advisory Committee, there is not sufficient 

confidence in the Tidal Peace changepoint analysis to develop a defensible numeric nutrient 

criterion. Therefore, as described in Figure 2-1, the reference period approach was recommended 

for developing a TN concentration criterion for Tidal Peace. As the segment is classified as 

“restoration” for seagrass, the TN concentration criterion is calculated by summing the annual mean 

from the reference period (2003-2007) plus 1⁄2 standard deviation (for the period of record): 

 

TN criterion = 0.99 mg/l (mean) + 1⁄2 * 0.18 (SD) = 1.08 mg/l 

A comparison of the candidate numeric TN concentration criteria for Tidal Peace based on the 

Reference Period method is presented in Figure 2-7. 
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Figure 2-7. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in Tidal Peace. 

2.6 Pine Island Sound and Matlacha Pass 

Based on discussions with the CHNEP Technical Advisory Committee, there is not sufficient 

confidence in the Pine Island Sound and Matlacha Pass regressions to develop defensible numeric 

nutrient criteria due to the amount of variability left unexplained by the regressions. Therefore, as 

described in Figure 2-1, the reference period approach was recommended for developing TN 

concentration criteria for Pine Island Sound and Matlacha Pass. As Pine Island Sound is classified 

as a seagrass “protection” segment, the TN concentration criterion is calculated by summing the 

annual mean from the reference period (2003-2007) plus one standard deviation (for the period of 

record): 

 

TN criterion = 0.46 mg/l (mean) + 0.11 (SD) = 0.57 mg/l 

Matlacha Pass is classified as a seagrass “restoration” segment, therefore the TN concentration 

criterion is calculated by summing the annual mean from the reference period (2003-2007) plus 1⁄2 

standard deviation (for the period of record): 

TN criterion = 0.53 mg/l (mean) + 1⁄2 * 0.10 (SD) = 0.58 mg/l 

A comparison of the candidate numeric TN concentration criteria for Pine Island Sound and 

Matlacha Pass based on the Reference Period method are presented in Figure 2-8 and Figure 2-9, 

respectively. 
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Figure 2-8. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in Pine Island Sound. 

Figure 2-9. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in Matlacha Pass. 
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2.7 San Carlos Bay and Tidal Caloosahatchee 

Based on discussions with the CHNEP Technical Advisory Committee, there is not sufficient 

confidence in the Tidal Caloosahatchee regression to develop a defensible numeric nutrient 

criterion due to the amount of variability left unexplained by the regression. Therefore, as 

described in Figure 2-1, the reference period approach was recommended for developing TN 

concentration criteria for Tidal Caloosahatchee. As San Carlos Bay is classified as “protection” for 

seagrass, the TN concentration criterion is calculated by summing the annual mean from the 

reference period (2003-2007) plus one standard deviation (for the period of record): 

 

TN criterion = 0.46 mg/l (mean) + 0.10 (SD) = 0.56 mg/l 

Tidal Caloosahatchee is classified as a seagrass “restoration” segment, therefore the TN 

concentration criterion is calculated by summing the annual mean from the reference period (2003-

2007) plus 1⁄2 standard deviation (for the period of record): 

TN criterion = 1.00 mg/l (mean) + 1⁄2 * 0.18 (SD) = 1.09 mg/l 

A comparison of the candidate numeric TN concentration criteria for San Carlos Bay and Tidal 

Caloosahatchee based on the Reference Period method are presented in Figure 2-10 and Figure 2-

11, respectively. 

Figure 2-10. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in San Carlos Bay. 
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Figure 2-11. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in Tidal Caloosahatchee. 

Tidal Caloosahatchee has been identified as impaired and a TMDL has been drafted. However, 

due to concerns raised with the draft TMDL for the Tidal Caloosahatchee, the TMDL is currently 

being revised. Therefore, it was decided to list the nutrient criteria for Tidal Caloosahatchee as “to 

be determined” (TBD) until the revision to the draft TMDL is completed.

2.8 Estero Bay 

Based on discussions with the CHNEP Technical Advisory Committee, there is not sufficient 

confidence in the use of the changepoint analysis to develop a defensible numeric nutrient 

criterion. Therefore, as described in Figure 2-1, the reference period approach was recommended 

for developing a TN concentration criterion for Estero Bay. As Estero Bay is classified as 

“restoration” for seagrass, the TN concentration criterion is calculated by summing the annual mean 

from the reference period (2003-2007) plus 1⁄2 standard deviation (for the period of record). This 

results in the following TN concentration criterion for Estero Bay: 

TN criterion = 0.57 mg/l (mean) + 1⁄2 * 0.12 (SD) = 0.63 mg/l 

A comparison of the candidate numeric TN concentration criterion based on the Reference Period 

method is presented in Figure 2-12. 
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Figure 2-12. Comparison of the candidate TN criterion to observed TN concentrations (expressed as 

arithmetic means) in Estero Bay. 

2.9 Recommended Numeric Nutrient Criteria as TN Concentrations 

Based on the results presented above, Table 2-2 provides the recommended numeric nutrient 

criteria as TN concentrations for the CHNEP. 

Table 2-2. Candidate numeric nutrient criteria based on the 

reference period approach for TN concentration.

Segment Candidate Criterion

Dona and Roberts Bays 0.42 mg/l

Upper Lemon Bay 0.56 mg/l

Lower Lemon Bay 0.62 mg/l

Tidal Myakka 1.02 mg/l

Tidal Peace 1.08 mg/l

Charlotte Harbor Proper 0.67 mg/l

Matlacha Pass 0.58 mg/l

Pine Island Sound 0.57 mg/l

Tidal Caloosahatchee TBD

San Carlos Bay 0.56 mg/l

Estero Bay 0.63 mg/l
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3.0 Total Phosphorus Concentrations 

As described in Janicki Environmental (2011b), multiple analyses were completed in the evaluation 

of potential TP criteria expressed as in-bay concentrations. The first set of analyses was performed 

to evaluate potential methods of deriving TP concentration criteria commensurate with the 

recommended TN concentration criteria and/or chlorophyll a thresholds. These included: 

 examination of the relationships between TN and TP concentrations within each segment, 

following the rationale that the recommended TN concentration criteria had already been 

developed (Janicki Environmental, 2011a) and relationships between TN and TP 

concentrations could provided TP concentration criteria; 

 examination of relationships between monthly TP concentrations with chlorophyll a

concentrations, with the potential to derive TP concentration criteria based on chlorophyll a

thresholds; and 

 application of a reference period approach to establishing TP concentration criteria. 

The most appropriate method was determined to be the Reference Period approach. Relationships 

between segment TN concentrations and segment TP concentrations are not transparent, and thus 

could not be used to translate the recommended TN concentration criteria to TP concentration 

criteria. Stressor-response relationships between chlorophyll a and TP concentrations were not 

sufficient to derive TP concentration criteria based on established chlorophyll a thresholds (Janicki 

Environmental, 2011b). It was determined that the Reference Period Approach (2003-2007) 

provided the most suitable and internally consistent method for establishing TN and TP 

concentration criteria for the CHNEP segments, with the exception of the Tidal Caloosahatchee. 

The Tidal Caloosahatchee has been determined to be impaired for nutrients and a draft TMDL has 

been developed. However, the TMDL is being revised due to concerns raised by stakeholders. 

The criteria for Tidal Caloosahatchee are “to be determined” until the TMDL revision is completed. 

Following this approach, numeric nutrient criteria expressed as TP concentrations for the bay 

segments were derived. Targets were based on 2003-2007 reference period data, and the standard 

deviations in each segment were based on the annual means. The recommended TP concentration 

threshold for each segment is provided in Table 3-1. The proposed TP concentration criteria are 

compared to the observed arithmetic mean annual TP concentrations in Figures 3-1 through 3-10, 

for all segments except the Tidal Caloosahatchee, as criteria for this segment are “to be 

determined”, as described above. The horizontal lines on the figures represent the recommended 

criteria. 
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Table 3-1. TP concentration criteria derived using the Reference 

Period Approach. The reference period was 2003-2007.

Segment TP concentration criterion

(mg/L)

Dona and Roberts Bay 0.18

Upper Lemon Bay 0.26

Lower Lemon Bay 0.17

Charlotte Harbor Proper 0.19

Pine Island Sound 0.06

San Carlos Bay 0.07

Tidal Myakka River 0.31

Tidal Peace River 0.50

Matlacha Pass 0.08

Tidal Caloosahatchee River TBD

Estero Bay 0.07

Figure 3-1. Comparison of proposed TP concentration criterion for Dona and Roberts Bay to the annual 

arithmetic mean TP concentrations. 
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Figure 3-2. Comparison of proposed TP concentration criterion for Upper Lemon Bay to the annual 

arithmetic mean TP concentrations. 

Figure 3-3. Comparison of proposed TP concentration criterion for Lower Lemon Bay to the annual 

arithmetic mean TP concentrations. 
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Figure 3-4. Comparison of proposed TP concentration criterion for Charlotte Harbor Proper to the annual 

arithmetic mean TP concentrations. 

Figure 3-5. Comparison of proposed TP concentration criterion for Pine Island Sound to the annual 

arithmetic mean TP concentrations. 
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Figure 3-6. Comparison of proposed TP concentration criterion for San Carlos Bay to the annual 

arithmetic mean TP concentrations. 

Figure 3-7. Comparison of proposed TP concentration criterion for Tidal Myakka River to the annual 

arithmetic mean TP concentrations. 
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Figure 3-8. Comparison of proposed TP concentration criterion for Tidal Peace River to the annual 

arithmetic mean TP concentrations. 

Figure 3-9. Comparison of proposed TP concentration criterion for Matlacha Pass to the annual arithmetic 

mean TP concentrations. 
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Figure 3-10. Comparison of proposed TP concentration criterion for Estero Bay to the annual arithmetic 

mean TP concentrations. 

4.0 Total Nitrogen and Total Phosphorus Loadings 

As described in Janicki Environmental (2011b), the simplest method to propose criteria expressed 

as loadings to bay segments is based on relationships between segment TN and TP concentrations 

and TN and TP loadings delivered to each segment. The recommended TN concentration criteria 

and TP concentration criteria described above can be compared to TN and TP loadings to the 

segments. If significant relationships are found between the nutrient loads and their respective 

segment concentrations, then the proposed numeric nutrient criteria could be expressed as 

loadings. However, based on the limited relationships found between the nutrient concentrations 

and nutrient loads to those segments, the results of these analyses do not provide adequate 

evidence to support recommendations for TN and TP loading criteria. 

A second method evaluated to provide potential TN and TP criteria expressed as loadings to bay 

segments is based on relationships between segment chlorophyll a concentrations and TN and TP 

loads delivered to each segment. Chlorophyll a thresholds have been developed for the SBEP 

(Janicki Environmental, 2011a), and may be used to derive loading criteria if appropriate 

relationships exist. The results of these analyses did not provide adequate evidence to support 

recommendations for TN and TP loading criteria based on the relationships between chlorophyll a

concentrations and TN and TP loadings in the bay segments. 

Establishment of loading-based nutrient criteria should be consistent with the chlorophyll a

threshold and concentration-based TN and TP criteria already recommended for the Charlotte 

Harbor National Estuary Program area. The third approach to developing loadings-based numeric 
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nutrient criteria for both TN and TP is the reference period approach. Based on the methods used 

for development of the chlorophyll a threshold and the recommended TN and TP concentration 

criteria, loading targets and thresholds were developed. As with nutrient concentrations, the 

reference period was 2003-2007. Because loading data are available through 2007, the period 

used to calculate the standard deviation was 1995-2007. These loading criteria (thresholds) are the 

sum of the 2003-2007 mean and one standard deviation. These criteria are considered to be 

commensurate with reference period TN and TP concentrations, and with the reference period 

chlorophyll a thresholds developed previously (Janicki Environmental, 2011a). The loading criteria 

for TN and TP are presented in Table 4-1. The proposed TN and TP loading criteria are compared 

to the observed annual TN and TP loadings in Figures 4-1 through 4-10 for all segments except 

Tidal Caloosahatchee. The horizontal lines represent the proposed criteria. 

Table 4-1. TN and TP loading criteria based on the Reference Period 

Approach. The reference period was 2003-2007.

Segment TN Load

(tons/yr)

TP Load

(tons/yr)

Dona and Roberts Bay 250 48

Upper Lemon Bay 102 18

Lower Lemon Bay 136 21

Charlotte Harbor Proper1 5,987 2,281

Pine Island Sound 190 8

San Carlos Bay TBD TBD

Tidal Myakka River 1,407 351

Tidal Peace River 4,343 1,960

Matlacha Pass 216 24

Tidal Caloosahatchee River TBD TBD

Estero Bay 587 61

1

Loads are sum of Charlotte Harbor Proper and the Tidal Peace and Myakka Rivers.
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Figure 4-1. Comparison of proposed TN and TP load criteria for Dona and Roberts Bay to annual loads.
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Figure 4-2. Comparison of proposed TN and TP load criteria for Upper Lemon Bay to annual loads.
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Figure 4-3. Comparison of proposed TN and TP load criteria for Lower Lemon Bay to annual loads. 
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Figure 4-4. Comparison of proposed TN and TP load criteria for Charlotte Harbor to annual loads. 
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Figure 4-5. Comparison of proposed TN and TP load criteria for Pine Island Sound to annual loads. 
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Figure 4-6. Comparison of proposed TN and TP load criteria for San Carlos Bay to annual loads. 
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Figure 4-7. Comparison of proposed TN and TP load criteria for Tidal Myakka to annual loads. 
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Figure 4-8. Comparison of proposed TN and TP load criteria for Tidal Peace to annual loads. 
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Figure 4-9. Comparison of proposed TN and TP load criteria for Matlacha Pass to annual loads. 
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Figure 4-10. Comparison of proposed TN and TP load criteria for Estero Bay to annual loads. 
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5.0 References 

Janicki Environmental, Inc. 2009. Water Quality Target Refinement Project – Task 2: Seagrass 

target development. Interim Report 2. Prepared for Charlotte Harbor National Estuary Program, Ft. 

Myers, FL. Authors: Janicki, A., M. Dema, and M. Wessel. 

Janicki Environmental, Inc. 2010. Empirical Approaches to Establishing Numeric Nutrient Criteria 

for Southwest Florida Estuaries. Prepared for Tampa Bay Estuary Program, Sarasota Bay Estuary 

Program, and Charlotte Harbor National Estuary Program. 

Janicki Environmental, Inc. 2011a. Development of Numeric Nutrient Criteria for the Estuarine 

Waters of the Charlotte Harbor National Estuary Program. Task 7: Numeric Nutrient Criteria 

Development Interim Report 6. Prepared for Charlotte Harbor National Estuary Program, Fort 

Myers, FL. 

Janicki Environmental, Inc. 2011b. Charlotte Harbor Numeric Nutrient Criteria: Task 8 – TN and 

TP Loading and Concentration Based Criteria. Letter Memorandum. Prepared for Charlotte Harbor 

National Estuary Program, Fort Myers, FL. 
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APPENDIX C. 

Implementation Issues: 

Targets, Thresholds, Type I Error and 

Compliance Assessment for Numeric Nutrient Criteria 

Using the Reference Period Approach 

Background 

Site specific numeric nutrient criteria for individual estuarine water bodies in southwest Florida 

from Saint Joseph Sound in Clearwater, Florida through Estero Bay, Florida are being proposed as 

alternatives to the application of regional or state wide model based standards. These site specific 

criteria rely on the identification of a response endpoint and the endpoint defined for these 

estuaries has been defined as a threshold chlorophyll a concentration in all cases. The temporal 

scale has been defined as yearly; therefore, the assessment statistic is an annual average chlorophyll 

a concentration. Generally, the geometric annual average is used; however, in cases where the data 

are first averaged monthly, a simple arithmetic average is used. These threshold chlorophyll a

concentrations for all estuaries have been identified using a reference period approach. Subsequent 

numeric nutrient criteria have been developed either by applying a stressor response relationship 

between nutrients and chlorophyll a concentrations, or by simply calculating an average of the 

annual averages of a defensible reference period. 

The reference period approach relies on the identification of a period in time when these estuarine 

water bodies were sufficient to support full aquatic life uses. The overarching logic is that, provided 

a reliable stressor response model cannot be developed to accurately predict that point at which a 

system would no longer meet its full aquatic life use, water quality conditions during of a period in 

time when that waterbody was meeting its designated use would be protective of full aquatic life 

uses. For example, the estuarine open water segment of Saint Joseph Sound has been meeting full 

aquatic life uses according to FDEP water quality standards and the Impaired Waters Rule since 

2003. This means that chlorophyll a concentrations (Chla) have been below an annual average of 

11 μg/L and dissolved oxygen concentrations (DO) have been above 4 mg/L in at least 90% of the 

samples. These “endpoints” (i.e., Chla and DO) are typical indicators used to assess the health of 

estuarine waters. The period of time between 2003 and 2007 was therefore chosen as the reference 

period for the CHNEP. 

To establish numeric nutrient criteria using the reference period approach, a period of time would 

be identified when the waterbody was meeting its designated use, parameters would be defined to 

characterize the population of water quality values for chlorophyll a, total nitrogen (TN) and total 

phosphorus (TP) during that time, and then threshold values would be defined to represent a 

deviation from the expected condition of the reference period. The following paragraphs provide 

an example of how targets, thresholds and the type I error, and compliance assessment procedures 

have been established using the reference period approach. 

Reference Period Example 

To begin this example, a hypothetical reference period distribution of chlorophyll a concentrations 

was generated. Chlorophyll a concentrations in estuaries typically exhibit “lognormal” distribution 

characteristics. This implies that when a natural log transformation is applied to the distribution, it 
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becomes normally distributed which conforms to most parametric statistical tests. Therefore, a 

lognormal distribution of chlorophyll a concentrations was simulated using a mean of 6.75 μg/L 

and a standard deviation of 4.49 μg/L. This distribution composed of 10000 observations is shown 

in Figure 1. Once the data are natural log transformed, the distribution becomes bell shaped 

corresponding to the normal distribution (Figure 2). Since the Florida Department of Environmental 

Protection (FDEP) and the Environmental Protection Agency (EPA) have proposed using annual 

geometric means as regulatory statistics for parameters with lognormal distributions such as 

chlorophyll a, we now consider the log transformed values to represent the data underlying this 

hypothetical evaluation and back transform the averages to obtain the geometric means. 

Given the theoretical distribution of Figure 2, we can generate annual averages to simulate the 

product of a typical monitoring program. For example, we can randomly select 12 observations 

from the distribution of log values, and calculate an average and back transform that average to 

obtain the geometric mean. Further, we can repeat this experiment many times, each time 

selecting 12 samples and calculating the average of the log values. We expect each average to be 

close to the overall average of the reference period since it is a random sub-sample, however, we 

know that variability will exist due to sampling. For example, in Figure 3, we have generated 100 

annual averages from the reference period distribution. As can be seen in Figure 3, the distribution 

of annual averages is centered on a value very close to the overall average in Figure 2 which is 

expected. 

Figure 1. Simulated distribution of chlorophyll a concentrations. 
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Figure 2. Distribution of the natural log transformed values of the simulated distribution above. 

Figure 3. Distribution of 100 annual averages of the log transformed chlorophyll values using 12 samples 

per year. 
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To derive the geometric annual averages, we simply back transform the annual averages of Figure 

3. This distribution is shown in Figure 4. 

Figure 4. Geometric means taken from the simulated chlorophyll concentrations above. 

Targets and Thresholds 

Once the geometric means have been calculated we have all the information necessary to develop 

targets and thresholds for this theoretical reference period distribution. 

 

The reference period target for this distribution can be defined as the overall average of all the 

geometric means. That is, 5.947 μg/L is our goal for the water body to ensure that it remains similar 

to the reference period condition we identified as being indicative of full aquatic life support. 

However, it can be seen from Figure 4 that the distribution of annual geometric means for this 

population ranges between 3.9 μg/L and 8.3 μg/L. Therefore, the distribution of geometric means 

can be considered a population of values that represent the expected distribution of annual 

averages of the reference period. Based on normal distribution theory, we can assign a threshold 

value to represent an annual average above which we would reject the hypothesis that the value 

was from the same population as the reference period distribution of annual geometric means. 

Using the z table of standard statistical tests, only 5% of a normal distribution with a mean and 

standard deviation of the distribution in Figure 4 would lie above the mean+1.65*the standard 

deviation of the population of geometric means. Therefore, a threshold can be constructed for this 

distribution that defines with 95% confidence what value a given geometric mean would need to 

exceed to reject the hypothesis that it belonged to the reference period distribution. For this 

distribution that threshold value equals 7.59 μg/L. 
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The threshold value provides a level of certainty that a future single geometric mean value (i.e. a 

sample) is not declared to exceed the reference distribution simply due to sampling. As was 

demonstrated above, we know that some portion of the reference distribution values will be above 

the target value. In fact, nearly 50% of the annual geometric means will be higher than the target. 

However, only 5% of the values will be higher than the threshold value of 7.59 μg/L due to 

chance. This construct defines what is known as the Type I error rate or False Positive rate. That 

is, we are willing to accept that 1 in 20 times we may get a value that is higher than 7.59 μg/L that 

still belongs to the reference period distribution. As was seen in Figure 4, 5% of the values did 

exceed 7.59 μg/L even though we know the entire population of values. 

Therefore, the type I error rate is a value that is selected based on judgment and while 5% is 

typically used, there is no definitive rationale for 5% versus 1% or 10%. If we wish to be more 

conservative, we would select a lower type I error rate by choosing a larger value (e.g., 1.96) to 

multiple against the standard deviation to minimize the potential for falsely declaring that a value 

was different from the reference distribution. If we have reason to believe that the water body may 

not fully meet its designated use at values at the higher end of the reference distribution, one could 

select a higher type I error rate which in turn would equate to a smaller z score to multiply by the 

standard deviation (e.g., 1). For example, selecting 1 standard deviation equates to a type 1 error 

rate of 16%. However, the type 1 error rate does have implications on the compliance assessment. 

Compliance Assessment 

 

Now that the definition of targets, thresholds, and type 1 error has been identified, there is another 

consideration that must be taken into account when evaluating criteria exceedances. The 

exceedance frequency for an exceedance due to chance is defined by the type 1 error rate as 

described above. However, the exceedance frequency and duration component also must be 

established to allow for some anomalous condition unrelated to anthropogenic activity such as an 

El Niño, or La Niña cycles. There is substantial evidence that these meteorological anomalies can 

result in higher chlorophyll a concentrations (e.g., Morrison et al. 2006, Sherwood 2010). 

Therefore, this type of exceedance is different from the type I error described above. Since we have 

previously defined the type I error rate, we have already made the choice as to the false positive 

rate we are willing to accept. The implementation question is now posed to ask “what is the 

frequency of exceedances and assessment cycle that allows for occurrences unrelated to local 

anthropogenic activities but remains sensitive to capturing population deviations from the reference 

period due indicative of human adverse effects?” 

To address this question the Multivariate ENSO Index calculated by Klaus Wolter of the National 

Oceanic and Atmospheric Administration (see Wolter and Timlin 1993) was used as described in 

several implementation documents produced by Janicki Environmental regarding implementation 

of numeric nutrient criteria (Janicki Environmental, Inc. 2011a-c). It is easy to see in Figure 5 that 

when El Niño or La Niña events occur they tend to last more than a single year. In fact, it’s quite 

possible for many of the single events to cross a calendar year. Further information on the 

frequency and duration of ENSO events can be found at: http://www.esrl.noaa.gov/psd/enso/mei/
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Figure 5. Classification of El Niño and La Niña events as described in Janicki Environmental 2011a.

Based on this analysis, it makes sense to allow for the potential that an anomalous event could 

result in higher annual geometric average than the reference period threshold value in more than 

one year in a 5 year cycle as is currently proposed by FDEP. Therefore the recommended 

allowance as an exceedance frequency in a five year assessment cycle is to allow for no more than 

2 exceedances in a 5 year assessment cycle. 

It is possible that the type I error rate and the probability of an anomalous event can be calculated 

such that both the probability of an exceedance occurring by chance and the probability that an 

exceedance occurs due to anomalous conditions could be integrated. That is, over a 5 year cycle 

one might calculate the union probability of an exceedance due to chance and an exceedance due 

to a natural anomaly. This was beyond the scope of this memorandum but one that might be 

pursued as the implementation process is refined. Because the proposed criteria are based on 

threshold values with known type 1 error rates, the criteria and the 2 in 5 year implementation 

criteria are inextricably linked and should not be separated. Further information supporting the use 

of the 2 in 5 implementation rule is provided in Janicki Environmental (2011a-c). 
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References 

Janicki Environmental, Inc. 2011a. Sarasota Bay Numeric Nutrient Criteria: Task 4 - 

Implementation Issues. Letter Memorandum Prepared for Sarasota Bay Estuary Program. Sarasota, 

Florida 

Janicki Environmental, Inc. 2011b. Charlotte Harbor Numeric Nutrient Criteria: Implementation 

Issues. Letter Memorandum Prepared for Charlotte Harbor Estuary Program. Ft. Myers, Florida 

Janicki Environmental, Inc. 2011c. Tampa Bay Numeric Nutrient Criteria: Task 4 –

Implementation Issues. Letter Memorandum. Prepared for: Tampa Bay Estuary Program. 

Morrison, G., E.T. Sherwood, R. Boler, and J. Barron. 2006. Variations in water clarity and 

chlorophyll a in Tampa Bay, Florida, in response to annual rainfall, 1985-2004. Estuaries and 

Coasts. 29:926-931.

Sherwood, E.T. 2010. 2009 Tampa Bay Water Quality Assessment. 2010. Technical Report #02-10 

of the Tampa Bay Estuary Program. Prepared by the Tampa Bay Estuary Program. 

Wolter, K., and M.S. Timlin, 1993: Monitoring ENSO in COADS with a seasonally adjusted 

principal component index. Proc. of the 17th Climate Diagnostics Workshop, Norman, OK, 

NOAA/NMC/CAC, NSSL, Oklahoma Clim. Survey, CIMMS and the School of Meteor., Univ. 

of Oklahoma, 52-57.

Download PDF.http://www.esrl.noaa.gov/psd/people/klaus.wolter/MEI/#ref_wt1
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APPENDIX D. 

Maps of Monitoring Sites Utilized 

For Water Quality Assessment 

In Each Segment 
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D-3
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D-5
D-6
D-7
D-8
D-9
D-10
D-11
D-12
D-13
D-14
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