1

DEP’s Responses to EPA’s Questions and Requests for Clarification

Lakes

 Please provide a map and corresponding list of the names or WBIDS of lakes that would be 

covered under these criteria.

A spreadsheet listing the lake WBIDs and a map are attached.

 Please provide a description of how the decisions made to derive the numeric criteria 

ensure that balanced natural populations of aquatic flora and fauna are supported in these 

waters at the criteria concentrations and that the designated uses of fish consumption, 

recreation and the propagation of fish and wildlife are protected. 

DEP addressed this in detail in the TSD (p. 161) and recommended Proposed Final Order

(p. 28, p.33). Maintaining lakes at their historic oligo- to meso-trophic condition is 

inherently protective of the fish consumption, recreation and the propagation of fish and 

wildlife that would occur under these natural nutrient levels. 

 For high colored lakes in the West Central region, provide a specific justification for how the 

lakes would be protected by the criteria calculated specific to streams

DEP addressed this in detail in the TSD (p. 187). The University of Florida requested that 

we assess the effectiveness of lake regions in explaining the chlorophyll response to 

nutrients for various parts of the state. DEP conducted a residuals analysis and found that 

the statewide regression between TP and chlorophyll was inaccurate for lakes in the West 

Central, high phosphorus region of the state (see below). After more closely examining 

the lakes in this geologic area (which was best explained by aggregating the lakes to 

match the West Central Stream Nutrient region), we re-ran the TP versus chlorophyll 

regression and applied an upper prediction interval. The upper prediction interval for the

lakes TP would have actually been higher than the streams criteria, so we capped the TP 

value at the TP value for streams in the region to ensure downstream protection.
2

Figure 1. As requested by the University of Florida, DEP conducted a regional analysis of 

residuals produced from the regressions between TP and chlorophyll. Because TP is 

clearly the limiting nutrient, the results show that TP concentrations in the West Central 

over-predicted the chlorophyll response.

Streams

 Provide a map and corresponding list of the names or WBIDS of flowing waters that would 

be covered under these criteria.

A spreadsheet listing the stream WBIDs and a map are attached.

 Provide a scientific justification for the changes made to the nutrient watershed region 

drainage areas (e.g., changes to West Central).

A description of the changes to the nutrient regions is provided in the TSD (p.86) and 

additional information is presented below for the main areas. 
3

Sarasota Area

The “Hydrogeologic Framework of the Southwest Florida Water Management District”, 

which was published in 2008 by the DEP (Arthur et al., Florida Geologic Bulletin No. 68) in 

cooperation with the SWFWMD, is the most up-to-date and thorough analysis of geology 

in this area. When mapped, the data show the phosphorus rich Hawthorn Formation to be 

widely distributed near the ground surface in Sarasota County (Figure 2). The data show 

Sarasota County to be influenced by naturally occurring phosphorus and that Sarasota Bay 

and Lemon Bay Watersheds should more appropriately be included in the West Central 

Nutrient Watershed Region than in the Peninsula (Figure 3). The analysis of the data from 

the 2008 geologic report clearly shows that phosphorus rich deposits are present in 

Sarasota County in both of the major coastal Estuarine Drainage Areas (EDA). Water 

quality data demonstrates that freshwater concentrations are very similar in the existing 

Peninsular and West Central Regions (Figure 4). Applying the Peninsular total phosphorus 

standards to the coastal EDAs will result in the erroneous conclusion that natural levels of 

phosphorus are due to anthropogenic inputs. 

Alachua County Area

After consulting with local scientists, DEP concluded that the areal extent over which 

water quality is influenced by naturally occurring phosphorus deposits in Alachua County 

was more extensive than either DEP or EPA originally realized. There is a group of “stream 

to sink” watersheds along the Central Florida Ridge that DEP ultimately included in the 

North Central NWR. After capture by the sinkholes, the groundwater flow in this area is 

to the north/northwest, toward the Santa Fe and Suwannee Rivers, both of which are in 

the North Central region (Figure 5). Based on direct observations by DEP staff, streams in 

this area down-cut through the phosphorus-rich Hawthorn Group and discharge to the 

Floridan aquifer through these active sink holes. 

Additional descriptions of the changes to the nutrient regions are provided in the TSD 

(p.86). 
4

Figure 2. Using 2008 data, the phosphorus rich Hawthorn Group covers a broad extent of Sarasota 

County including the coastal region.
5

Figure 3. Both coastal Estuarine Drainage Areas, Sarasota Bay and Lemon Bay, are influenced by 

the phosphorus rich Hawthorn Group.
6

Figure 4. Water samples from the West Central and Peninsular regions within Sarasota County 

show similar levels of TP. The geologic data indicate that Sarasota County should be entirely 

within the West Central region.
7

Figure 5. Recharge area for springs (dark blue line) in the Santa Fe basin. The “streams to sink” 

zone is within this geological catchment zone, where groundwater flows to the north/northwest

(after R. Knight, Santa Fe Springs Basin Working Group). 

 Provide a description of how the decisions made to derive the numeric criteria translate the 

narrative to ensure that balanced natural populations of aquatic flora and fauna are 

supported in these waters at the criteria concentrations and that the designated uses of fish 

consumption, recreation and the propagation of fish and wildlife are protected. 

Maintaining balanced flora and fauna of streams is inherently protective of fish 

consumption, recreation and the propagation of fish and wildlife. We addressed this in 

the TSD (p.133), the SCI Primer (Section 2.7), and the NNC Implementation Document (p. 

6).

 For the biological information used to interpret the narrative nutrient criteria, the 

corresponding guidance document needs specific numeric thresholds for metrics that 

measure chlorophyll a levels, algal mats or blooms, nuisance macrophyte growth, and 

changes in algal species composition that would provide clear, transparent and scientifically 

defensible decision-making points of where balance in aquatic flora and fauna is still 

supported.
8

Use of floral metrics is described in the SCI Primer (Section 2.7), and we have added 

decision keys and examples in the NNC Implementation Document (pp. 10-19).

 For the use of the SCI, provide a response to the issues raised in the EarthJustice’s 

Administrative Challenge (e.g., the poor correlation of this index to nutrient pollution and 

that waters have been listed as impaired due to nutrients at or above the selected SCI 

thresholds). 

There are poor correlations between nutrients and all biological response variables (both 

floral and faunal) because there are multiple confounding factors affecting the expression 

of nutrients. The SCI correlations (coefficient of determination) were similar to the floral 

correlations with nutrients, yet EPA is not questioning the relationship between nutrients 

and flora. If the SCI score is indicative of a healthy, well balanced faunal community, then 

it can be concluded that the stream is healthy, and that nutrients have not caused 

imbalance to the fauna. Flora is evaluated independently (see Implementation 

document). DEP’s standards require that healthy flora be present and that either the 

nutrient thresholds are attained or that fauna are demonstrated to be healthy via the SCI.

DEP would like to see specific examples of waterbodies that have been listed as impaired 

but with passing SCI scores. None were identified during the State Administrative Hearing. 

To the contrary, DEP has identified waterbodies (e.g., Santa Fe River) that attain the 

nutrient thresholds, but imbalances of flora have been expressed (algal mats), 

subsequently leading to failing SCIs, making DEP’s assessment of flora and fauna more 

protective than relying on the thresholds alone.

 For the use of the biological information in the streams assessment, provide a response to 

the issue raised in the Administrative Challenge regarding how the criteria ensure protection 

when all pathways are not considered, such as heterotrophic eubacteria that affects 

recreational uses. 

This topic was addressed in the TSD (p.110). The hypothesis was presented that 

heterotrophic bacterial respiration (Biochemical Oxygen Demand) is stimulated via 

nutrients, even when light is limiting, potentially resulting in lower Dissolved Oxygen. DEP 

independently applies its DO (and related BOD) standard to assure full protection of 

aquatic resources.

 Provide a description of how and explanation that provides assurance that high quality 

waters will be protected by these criteria (e.g., Florida Outstanding Waters)

This was addressed in the TSD (p. 5) and the Recommended PFO (p. 90). Also, the IWR 

requires that no adverse trends in nutrients, chlorophyll or SCI and LVI be present, which 

is an additional protective component of Florida’s criteria (which is not present in EPA’s 

criteria).
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Springs

 Provide a map and corresponding list of the names or WBIDS of springs that would be 

covered under these criteria 

A spreadsheet listing the spring WBIDs and a map are attached.

 Provide a description of how the decisions made to derive the numeric criteria translate the 

narrative to ensure that balanced natural populations of aquatic flora and fauna are 

supported in these waters at the criteria concentrations and that the designated uses of fish 

consumption, recreation and the propagation of fish and wildlife are protected.

We extensively addressed this in the TSD (p.47).

NEP Estuaries

 Provide a map and corresponding list of names or WBIDS of estuarine waters that would be 

covered by these criteria. 

Maps of the estuary segments were provided previously, but we have yet to create a 

cross-walk between the estuary segments and WBIDs.

 Provide scientific justification for the segmentation used for the estuaries.

For the Tampa Bay system, the TBEP relied on their long-standing bay segmentation, 

which has been used for the federally approved TMDL and the subsequent 

implementation plan. The segmentation for Sarasota Bay was based on recommendations 

from the SBEP Technical Advisory Committee, which recognized that different seagrass 

targets and site-specific nutrient criteria were needed for each of the five bay segments of 

Sarasota Bay (see TSD for Sarasota Bay). For Charlotte Harbor, the estuarine system was 

divided into 14 estuarine segments with differing water quality and distinctive resource 

management conditions (see TSD for Charlotte Harbor, pp. 4, 6, and 7). The segments 

were developed under a separate work order and are summarized in Janicki 

Environmental (2009a). Clearwater Harbor/St. Joseph Sound segmentation followed 

morphological and geographic features, and resulted in dividing the open St. Joseph 

Sound to the north, and two Clearwater Harbor segments that are divided by the Highway 

586 causeway to the north and the Highway 60 causeway to the south.

 Provide a description of how the decisions made to derive the numeric criteria translate the 

narrative to ensure that balanced natural populations of aquatic flora and fauna are 

supported in these waters at the criteria concentrations and that the designated uses of fish 

consumption, recreation and the propagation of fish and wildlife are protected. 

As described in the Marine Overview TSD, Florida’s estuaries and coastal systems are 

subject to an assortment of freshwater sources, and are characterized by wide variations 
10

in geology, bathymetry, driving forces, and ecological system organization. These differing 

influences result in a range of characteristic biological communities, each of which must 

be understood in the context of potential nutrient responses. Florida’s estuarine 

ecosystem types range from river-dominated alluvial systems (e.g., Apalachicola Bay), to 

those characterized by extensive seagrass communities (e.g., Apalachee Bay), salt marshes 

(e.g., Tolomato–Matanzas Rivers), or mangroves (e.g., Southwest Coast), to those with 

inputs from blackwater rivers (Nassau–St. Marys Estuaries), to those where coral reefs are 

the dominant feature (e.g., Florida Keys and Southeast Coast). Because of the diversity of 

Florida’s marine systems, the Department pursued an “estuary-specific” approach, where 

all existing information for each individual estuary was synthesized, and criteria were 

based on the ecological endpoints most relevant for each particular system. 

Under this “estuary-specific” approach, the Department first identified the major 

estuarine/coastal systems in Florida and then synthesized all available, relevant 

information for each distinct area. The Department, working with local scientists, then 

identified the most sensitive, valued ecological attributes for each system and 

subsequently determined the nutrient regime that would result in the protection of that 

resource (maintaining full support of aquatic life use). The following information was 

compiled for each individual estuary or marine system throughout the state: 

• A physical/chemical description of each system, including causal parameters 

(nutrients) and supporting variables (hydrodynamics, water residence time, 

transparency, salinity, dissolved oxygen [DO], etc); 

• A biological description of each system, including key biological response variables. 

The type, quality, community structure, and areal extent of valued ecological 

attributes were documented, emphasizing those expected to respond to 

anthropogenic nutrient enrichment, including seagrass, coral, hardbottom, 

phytoplankton, epiphytes, benthic invertebrates, and fish; 

• The main sources of nutrients, including any point sources and dominant land uses in 

the watershed; 

• The available scientific evidence quantifying the relationship between anthropogenic 

nutrient inputs and adverse effects on biological communities, including both primary 

responses (e.g., excess phytoplankton or macroalgal growth) and secondary responses 

(e.g., reduction in depth to seagrass, etc.); 

• Existing regional nutrient loading and hydrodynamic models, especially those able to 

predict the fate and transport of nutrients to estimate assimilative capacity; and 

• Proposed numeric targets needed for protecting or restoring the system, including a 

demonstration of the bases for the nutrient targets. 

Each individual estuary reports contains the details of the weight of evidence approach 

used by the Department to ensure that balanced natural populations of aquatic flora and 

fauna are supported.
11

 Provide a demonstration of how the criteria concentrations were calculated (data set used, 

descriptions of any screening, etc.) 

This is detailed in the individual Estuary Reports.

 For these waters specifically, there were different decisions made to calculate the criteria in 

each of the 4 estuarine systems -- a scientific justification is needed that demonstrates the 

appropriateness of those decisions (e.g., the use of standard deviations and standard 

errors).

This was discussed by Tony Janicki during a teleconference between EPA, DEP, TBEP, and 

Janicki Environmental. Mr. Janicki explained that in each system, there were different 

amounts of data available, which influenced the variability in the data set, and that 

stakeholders in each system, following a deliberative process, identified the appropriate 

standard deviation to apply to ensure protection.

 Provide a clear description of what criteria would apply in tidally influenced areas 

This is addressed in the Marine Overview document (p.1, p.63) and additional information 

is provided here. Tidally influenced areas that alternate between fresh and marine waters 

form the primary hydrologic link between terrestrial /freshwater systems and estuaries. 

These areas are characterized by high biological productivity, significant ecological value, 

complex environmental gradients, and numerous interconnected processes. Because of 

the dynamic nature of the fluctuating salinity zone, characterized by interactions between 

materials derived from freshwater inputs (naturally derived nutrients and organic matter) 

and more oligotrophic marine waters, they are critical feeding grounds, spawning areas, 

and nursery habitats for many species of fish, shellfish, birds, waterfowl, and mammals 

(Sanger et al. 2008). 

During the development of the numeric nutrient criteria proposed by DEP, only stations 

from open estuarine areas were included in the statistical derivation, and tidally 

influenced areas that alternate between fresh and marine waters were specifically 

excluded because they represented a resource distinctly different from the remainder of 

the estuary. Available information indicates it is not appropriate to apply numeric 

nutrient criteria developed for the open water segments of estuaries to these 

low/fluctuating salinity tidal areas (see Eyre 1998 and Wolanski et al. 2004). The narrative 

nutrient criteria (no imbalances of flora or fauna) would continue to apply to these 

important nursery zones.

Due to the variability of freshwater inflows, the area and location of the low salinity zone 

varies seasonally in response to rainfall events and can undergo rapid change affecting 

physical, chemical, and biological variables (SFWMD 2009). As illustrated in Figure 6, 

material entering the Low/Fluctuating Salinity environment as it transitions towards the 

open water portion of the estuary first undergoes geochemical processes, associated with 

a turbidity maximum, and then biological processes, associated with a productivity 

maximum (Church 1986). Suspended sediments derived from terrestrial runoff are 

trapped in high concentrations near the freshwater/saltwater interface (Jassby 1995, Eyre 

1998, Lin and Kuo 2003, North and Houde 2001, 2003, North et al. 2005, Fain et al. 2001). 
12

Such zones of high turbidity characterize the upper reaches of partially mixed estuaries 

around the world (Schubel and Pritchard 1986). 

Adjacent to the turbidity maximum, nutrients and other compounds bound to sediments 

are released, resulting in high aquatic productivity (SFWMD 2009). Because the turbidity 

maximum suppresses primary production (due to light extinction), a productivity 

maximum typically develops further downstream in clearer waters (Fisher et al. 1988). 

The productivity maximum may be composed of several sub-areas including the 

chlorophyll a maximum area, followed by zones of high abundance of zooplankton, 

copepods, and fish larvae (Figure 6). These zones develop as the algae produced in the 

chlorophyll a maximum area are used as a food source by epibenthic feeders such as 

polycheates, mysids, and amphipods (Diaz and Schaffner 1990). In turn, these epibenthic 

feeders serve as food sources for larval and juvenile fishes. Many researchers have 

concluded that freshwater inputs containing nutrients help maintain this beneficial 

production (Fisher et al. 1988, Day et al. 1989, Montagna and Kalke 1992), with higher 

freshwater flows leading to higher yields of desirable species (Loneragan and Bun 1999). 

Figure 6. Conceptual representation of the low/fluctuating salinity zone and associated 

processes, transitioning to an open water estuary (from SFWMD 2009, adapted from Eyre 

1998).

A large number of marine species depend on estuaries during some part of their life cycle 

(Gunter 1961, Day et al. 1989). One of the most prominent ecological attributes of 

estuaries consists of their function as nursery areas for the larval and juvenile stages of 

many species, including commercially important fish and shellfish (Gunter 1961, Rozas and 

Hackney 1983, 1984, Odum et al. 1984, Jassby et al. 1995, Fain et al. 2001, North and 

Houde 2001, 2003, North et al. 2005, Yozzo and Diaz 1999). 
13

The low/fluctuating salinity zone is considered critical to the life histories of many 

organisms (Holmes et al. 2000, Hughes et al. 2000), because it provides habitat for a wide 

variety of adult and juvenile freshwater, estuarine, and marine fishes (Rozas and Hackney 

1983, Odum et al. 1984, 1988, Peterson and Ross 1991). Low salinity tidal wetlands 

provide nursery grounds for many anadromous and catadromous fishes, such as shad, 

herring (alosids), striped bass (Morone saxatilis), and eels (Anguilla rostrata) (Massmann 

1954). These tidal low salinity areas are characterized by increased concentrations of 

organic matter, derived from freshwater inputs and in situ production (Odum et al. 1984). 

Extensive tidal freshwater and low salinity systems are found in all the major estuarine 

systems in North America, such as the Columbia River, San Francisco Bay, Hudson River, 

Delaware Bay, Chesapeake Bay, Pamlico Sound, Albemarle Sound, and the St. Johns and 

St. Lawrence River estuary systems (Crumbs 1977, Odum et al. 1984, Diaz 1989, Diaz and 

Schaffner 1990, Jones et al. 1990, Weisberg et al. 1997, Kimmerer 2002). These tidal 

freshwater /low salinity systems have been identified in major European systems such as 

the Baltic Sea and Ele River (Leppakoski 1975, Wolff 1972, Pfannkuche et al. 1975, 

Pfannkuche 1980, 1981). 

The low/fluctuating salinity zone is known to provide an abundance of food sources and 

protection from predators to a broad array of micro- and macroinvertebrates and fish 

(Diaz and Schaffner 1990, Yozzo and Diaz 1999). Protection from marine predators is 

associated with both the low salinities and low visibility associated with suspended solids, 

color, and abundant phytoplankton (Chesney 1989, Kimmerer 2002). This protection may 

help explain why the smallest fish are typically found in low salinity tidal creeks (Gunter 

1961). Thus, low/fluctuating zones provide an exceptional habitat for small or larval 

fishes (Roman et al. 2001, North and Houde 2001, 2003, North et al. 2005). Janicki (2011) 

provides a summary of ecosystem services and nursery habitat functions provided by tidal 

creeks in southwest Florida. 

DEP has currently developed marine nutrient criteria for open water estuaries in the 

southern and southwestern areas of Florida. The low salinity tidal creeks that feed these 

systems are expected to exhibit higher nutrient and chlorophyll a levels than the open 

water estuary areas (Janicki 2011). For example, in a study of eight minimally disturbed 

tidal creeks in South Carolina, Dame et al. (2000) showed that summertime chlorophylls 

typically exceeded 10 ug/L, and were as high as 40 ug/L (Figure 7). In contrast, most 

Florida open water estuaries are characterized by annual chlorophyll a concentrations of 

less than 8 ug/L (Figure 8).
14

Figure 7. Background chlorophyll a concentrations (ugIL) from unnamed, minimally 

disturbed tidal creeks associated with North Inlet, South Carolina, from 1997 to 1998 

(triplicates shown) (from Dame et al. 2000).

0 2 4 6 8

Chla

1 2 3 4 5

Cluster

Figure 8. Boxplot of long-term geometric mean chlorophyll a for 75 open water, healthy 

estuarine segments, which were grouped into 5 clusters generated by an agglomerative 

cluster analysis (from FDEP 2010).
15

Sanger et al. (2008) found that chlorophyll a concentrations in minimally disturbed tidal 

creeks in the southeast US, surrounded only by marsh, averaged 40 ug/L. The authors also 

found that chlorophyll in tidal creeks surrounded by suburban and urban land uses was 

not statistically different than the natural systems, but that chlorophyll a and phosphorus 

in the tidal creeks was statistically higher than the downstream, open water estuary 

(Figure 9).

Figure 9. Phosphorus and chlorophyll a levels by land use class and longitudinal gradient 

in selected southeast US estuaries. Bars represent average concentrations with one 

standard error (from Sanger et al. 2008)

This higher input of nutrients and organic matter is an essential operational component of 

the low/fluctuating salinity zone, and is a critical reason that tidal creeks provide vital 

ecosystem services (habitat, nursery areas, and high secondary productivity). Because of 

the naturally higher organic matter inputs, tidal creeks are generally lower in dissolved 

oxygen (DO) than the surrounding estuary, making DO an inappropriate target for numeric 

nutrient criteria development in tidal creeks (Janicki, 2011).

For the reasons cited above, including that the fundamental nursery function of the 

low/fluctuating salinity zone involves a naturally higher nutrient and chlorophyll regime, 

the narrative nutrient criteria (no imbalances in flora or fauna) remains appropriate for 
16

these areas. Literature references for the discussion on salinity zones are provided in 

Attachment A.

 For Sarasota bay, provide a justification and explanation why different sets of values (i.e., 

values given in estuary table under section c and i) are needed and why this is necessary 

only for Sarasota Bay

See section 2.2 of the Sarasota Bay TSD, which describes how the relationship between 

nutrients and chlorophyll a in the Sarasota Bay segment is influenced by color, which in 

turn is related to swamp inputs.

 For Clam Bay (Collier county), a justification and explanation of the need for provision given 

in section J of the estuary table -- a scientific justification for the equation given and the 

appropriateness of these provision to protect designated uses only in Clam Bay

The basis and justification for the approach used for Clam Bay are described in the August 

31, 2011 Technical Note from David A. Tomasko, PhD to Gary McAlpin. Clam Bay appears 

to be co-limited by both TN and TP (PBS&J 2008). Consequently, salinity-normalized 

targets were developed for both TN and TP targets were. To be consistent with existing 

methodology used by DEP, the upper 10th prediction limit for the regression between TN 

or TP and conductivity (from Clam Bay) was used for target setting. The upper 10th 

prediction limit was selected in order to identify the number of TN and TP values at the 

corresponding conductivity that exceed the upper boundaries of the relationship. This 

approach is consistent with the calculation of the 10th percentile of DO values from 

reference waterbodies, as is used by DEP in ongoing target setting efforts. 

The relationships between conductivity (salinity) and nutrient concentrations were used 

to explain a portion of the temporal variance in TN and TP levels within Clam Bay. Use of 

this approach reduces both potential Type I and II statistical errors over a simple 

percentile approach used for other estuaries. DEP investigated a similar approach in other 

estuaries, but did not find sufficiently robust relationships. DEP intends to investigate this 

approach for future estuary criteria and expects to find some applicability in areas with 

significant variation in freshwater inflows. [Additional explanation of the derivation of the 

Clam Bay criteria was subsequently requested, and the additional information is provided 

on pages 18-24 of this document.]

South Florida marine

 Provide a map and corresponding list of the names or WBIDS of South Florida marine waters 

that would be covered by these criteria, and scientific justification for the segmentation.

The basis for the segmentation of South Florida estuaries was provided in the TSDs for 

each estuary. For example, see Appendix B in Biscayne Bay Report.

 Provide a demonstration of how the criteria concentrations were calculated (data set used, 

descriptions of any screening, etc.).
17

This was described in each estuary-specific report. The primary data set used to develop 

the criteria was the Florida International University’s South Florida Coastal Water Quality 

Monitoring Network available at http://serc.fiu.edu/wqmnetwork/SFWMDCD/index.htm. DEP downloaded the entire FIU data set directly from the website. Data 

queried from the IWR Run 44 and Florida Storet databases from Collier County and the 

City of Naples were also used to develop criteria for Naples Bay. The period of record 

used to derive criteria was generally 1995 to 2008, with a few exceptions. Data from 1995 

to 2005 were used for the Manatee Bay Barnes Sound segment. Additionally, FIU 

monitoring on the South West Coastal area was not initiated until 1999, thus the period of 

record for this area was 1999 to 2008.

Data were screened for fatal qualifier codes (J, Q, K, N, O, Y), and the data with these 

codes were excluded from the analysis. Any values reported as less than the method 

detection limit (MDL) were replaced with 1⁄2 the value of the reported MDL.

 Provide a description of how the decisions made to derive the numeric criteria translate the 

narrative to ensure that balanced natural populations of aquatic flora and fauna are 

supported in these waters at the criteria concentrations and that the designated uses of fish 

consumption, recreation and the propagation of fish and wildlife are protected.

The evidence considered by the Department in support of the “maintain healthy 

conditions approach” was described in individual reports (see PFO, p.53-69 for a 

summary).

All

 Provide an explanation how the duration and frequency components for each waterbody 

type ensure that balanced natural populations of aquatic flora and fauna are supported in 

these waters and that the designated uses of fish consumption, recreation and the 

propagation of fish and wildlife are protected.

This is extensively discussed in the TSD, p.193; and the PFO, p.30

Responses to Questions and Requests Provided by Phone in August, 2012

 What were the dates of the NNC TAC meetings when the lakes alkalinity classification 

threshold was discussed?

The lakes alkalinity classification threshold was discussed during the November 17, 2009 

meeting in Tampa, and during the April 7, 2010 meeting in Tallahassee. The TAC provided 

guidance that an alkalinity threshold of 20 mg/L CaCo3 was appropriate to distinguish 

chlorophyll expectations in naturally oligotrophic lakes from chlorophyll expectations in 

naturally mesotrophic lakes.

 Who at EPA did DEP ask to determine reference sites were the same for the floral 

measures? 
18

Jacques Oliver at EPA Headquarters sent FDEP a disc titled, “Final Rule TSD Data: File List 

and Description, Appendices A1, A3, and B1”, EPA-HQ-OW-2009-0596. FDEP only selected 

sites with floral information that were within the specific WBIDs used by EPA for their 

reference sites for calculating floral benchmark values for the weight of evidence 

approach. Therefore, DEP’s and EPA’s reference sites are the same.

 Provide an example/case study to illustrate how the trend analysis would be conducted and 

how it would help with downstream protection.

An example involving the Weeki Wachi River was inserted into the Implementation

document.

Questions on NNC for NEP Estuaries (to be addressed by Tony Janicki)

 Describe the process used to screen data for the SW coast NNC (including identifying and 

removing outliers, and excluding data from periods with impairments).

 Were there any WBIDs impaired during 92-94 used as the baseline for the Tampa Bay?

[Tony said there were none during the call, and I elaborated that Florida’s 1992 and 1994 

303(d) lists were simply the SWIM priority list.]

 What is the difference between a chl a target and chl a threshold? And how do we justify 

setting the criteria at the higher of the two?

 How were TN and TP concentrations specifically related to chlorophyll a levels that were 

protective of seagrass?

 What is basis for the formula-based criteria for Sarasota Bay, which takes into account color 

and location? [Tony explained verbally and may have assumed his response was sufficient.]

 Describe how the TN delivery ratio method will be implemented. [I prepared the 

explanation (see underlined text below), and Tony and Holly agreed it is accurate. I will add 

to implementation document]

The following text was inserted into the implementation document.

For the Tampa Bay estuarine system where nutrient standards are expressed as a delivery 

ratio, the Tampa Bay Estuary Program has agreed, pursuant to their binding Reasonable 

Assurance agreement, to provide the hydrologic and loading information (for both point 

and nonpoint sources) needed to calculate and assess annual delivery ratios on at least a 

five year frequency, which is consistent with DEPs watershed assessment cycle. However, 

TBEP has agreed to evaluate chlorophyll a targets on an annual basis, and will provide DEP 

with the needed information more frequently if chlorophyll a targets are exceeded for 

two consecutive years. 
19

 Clearly describe how the Clam Bay criteria were derived. What was the healthy reference 

period? Compare to other SW coast estuaries to show Clam bay criteria are protective.

DEP used a combination of relevant background information, a summary of existing 

studies on Clam Bay, and well-developed and scientifically appropriate empirical methods 

to develop NNC for Clam Bay. The methods used were consistent with prior studies 

conducted for the Tampa Bay, Sarasota Bay, and Charlotte Harbor National Estuary 

Programs. DEP determined that the existing nutrient conditions in Clam Bay (data from 

2006, 2009, 2010, and 2011) fully supported a healthy, well balanced aquatic community

(healthy existing conditions approach). Clam Bay, which is surrounded by intact mangrove 

forest, is similar to nearby, virtually pristine waterbodies, such as Fakahatchee Bay (which 

is fully within the Big Cypress National Preserve). Multiple studies, including water quality 

collection and analysis, pollutant loading model development, benthic invertebrate 

evaluation, toxin quantification and sediment accumulation rate assessments all indicate 

that Clam Bay is a healthy system. For example, sediment cores collected from 13 sites in 

Clam Bay showed low levels of organic enrichment, suggesting a lack of impact from algal 

blooms, and no sediment toxins in the Bay proper, also indicating healthy conditions.

While the bay’s healthy conditions made it a candidate for the “maintain healthy 

conditions approach” used by DEP for other South Florida estuaries, the Department 

decided not to use the standard statistical approach, which determines annual geometric 

mean values not to be exceeded more than once in three years, because nutrient 

concentrations showed significant variation with salinity. Based on historically observed 

differences in nutrients that were related to salinity at other nearby estuaries (e.g., Estero 

Creek wetlands), DEP explored salinity-adjusted criteria for Clam Bay and decided that 

salinity adjustment best explained the natural variability in the observed Clam Bay data. 

However, for NNC development, only data from within Clam Bay, collected during healthy 

conditions (2006, 2009, 2010, and 2011) and adjusted for salinity were used to establish 

future nutrient criteria expectations.

While the final Clam Bay criteria are expressed as a value not to be exceeded in more than 

10 percent of the samples, it should be noted that the annual geometric mean TN and TP 

values for Clam Bay are within the range of average values observed at other healthy 

estuaries in the southwest (Figure 13).
20

Figure 13. TN, TP and chlorophyll annual geometrics means at healthy southwest coast estuaries.

 Provide more explanation of Clam Bay segmentation, screening, MDLs, outliers, exclusions, 

and quality assurance.

The following was excerpted from a technical note provided by David A. Tomasko and 

Emily H. Keenan of Atkins and describes the methods used to review and develop the 

comprehensive water quality data base used to create the site-specific salinity-normalized 

Total Nitrogen (TN) and Total Phosphorus (TP) numeric nutrient criteria (NNC) for Clam 

Bay in Collier County:

Data within the database were either provided directly from Collier County staff or 

queried from IWR Run 42 data (supplied by FDEP). All available water quality data were 
21

subject to a quality assurance / quality control plan. At the time of this analysis, Clam Bay 

and Moorings Bay were both included in WBID 3278Q (Naples). As part of the 

development of the Clam Bay NNC, a comparison of water quality in Moorings and Clam 

Bay was completed, resulting in the creation of separate WBIDs for each waterbody. All 

water quality stations used for this analysis were displayed using GIS software to ensure 

that they were located within the revised Clam Bay watershed boundary. It is important 

to note that future water quality queries from FDEP IWR data will require retrieving data 

for WBID 3278Q1 (Clam Bay). For this effort, the majority of data utilized were 

contributed by the Collier County water quality monitoring efforts. 

Collier County Clam Bay Data 

The Collier County Coastal Zone Management Program collects monthly ambient water 

quality samples from nine stations located in Clam Bay. The Collier County staff have 

received Standard Operating Procedure certification from FDEP, and all sampling 

procedures are consistent with a Quality Assurance / Quality Control Plan. The initiation 

of the Clam Bay monitoring program began in November 2009. The monitoring program 

samples for the following parameters, including both water samples and sonde 

measurement (see Table below). 

Water Quality parameters included in Clam Bay Monitoring Program 

Parameter Unit Type 

BOD mg/L Grab Sample

Chlorophyll a mg/m3 Grab Sample

Coliform Fecal cfu/100ml Grab Sample

Color PCU Grab Sample

Enterococci cfu/100ml Grab Sample

Nitrate-Nitrite (N) mg/L Grab Sample

Nitrogen- Total Kjeldahl mg/L Grab Sample

Orthophosphate (P) mg/l Grab Sample

Pheophytin mg/m3 Grab Sample

Phosphorus- Total mg/L Grab Sample

Turbidity NTU Grab Sample

TN mg/L Grab Sample

Temperature C Sonde 

Specific Conductivity umhos/cm Sonde 

Salinity ppt Sonde 

The YSI sonde used to report water quality conditions was calibrated both prior and post 

field application by Collier County Coastal Zone Management staff to ensure viable data. 

All water quality grab samples are transported to the Collier County Pollution Control 

Laboratory for analysis. The monitoring data were provided to Atkins staff with qualifiers 

and relevant comments included. Quality control procedures were completed by both the 

Collier County Pollution Control Laboratory prior to data submittal and by Atkins staff 

prior to data utilization. 
22

Collier County Pollution Control Laboratory QA/QC 

Standard quality control (QC) procedures, data reduction, and reporting are in compliance 

with requirements in Standard Methods for Examination of Water and Wastewater, 20th 

ed., EPA Methods, Rule 62-160, F.A.C., and the 2003 NELAC Standards. The laboratory 

completes the following review to ensure accuracy prior to reporting the data to the client 

(Collier County Coastal Zone Management): 

 Data reduction is performed by either Excel worksheets or instrument software. 

Software is validated by the manufacturer prior to use. The laboratory supervisor 

audits the Excel calculations periodically during regular data review. 

 The primary responsibility for generation of accurate data rests with the analyst. The 

analyst performs the data calculation functions and is responsible for the initial 

examination of the finished data. Each analyst reviews their work based on the 

following guidelines: 

o The appropriate SOP has been followed. 

o Sample preparation is correct and complete 

o Analytical results are correct and complete 

o Blank correction procedures are followed, if applicable (i.e. silica and sulfate) 

o QC samples are within established QC limits 

o All documentation is complete 

 The QC procedures outlined in this quality assurance plan and the analytical SOPs are 

used for preliminary validation of results along with any historical data, if available. 

 After data reduction and validation steps are followed, the analyst submits the data 

into the appropriate client file. 

 The data is then reviewed by the laboratory quality assurance specialist, who 

evaluates the data along with pertinent QC results such as laboratory control 

standards, matrix spikes, duplicates, blind duplicates, blind performance evaluation 

samples, and laboratory performance records, as well as historical records to help 

form the basis for acceptance of data. The final review is based on the following 

criteria: 

o Calibration data review 

o Appropriate methodologies used

o QC samples within established guidelines 

o Comparison of historical data when available 

o Completion of all analytical work requested 

 After validation and review by the laboratory supervisor, the approved data is 

incorporated into a final analysis report. The final report is released to the submitter 

and the full data package is archived for possible future use. 

Errors or problems that occur are documented and maintained in the client file. The cause 

of the error is then addressed either by further training or re-evaluation of the analytical 

method SOPs to ensure quality data are generated at the analyst level. 

Atkins QA/QC 
23

The Clam Bay Collier County water quality data were provided to Atkins as an Excel 

workbook with field and analytical data on separate worksheets. Initially, the range for 

each parameter was reviewed to ensure accuracy of data. If outliers were identified, 

Collier County Coastal Zone Management staff was contacted and the data was validated 

by reviewing the field data sheet or laboratory result and corrections were made if 

justified. One TP data point was removed from the dataset as the concentration was 

elevated beyond the expected range for the region (June 17, 2010, station CB1, TP=0.957 

mg/L). The normal range of TP concentrations within Clam Bay are 0.018 to 0.175 mg/L. 

In review of the laboratory data the following data qualifier codes were reported for 

either TN or TP data used for the analysis: 

Qualifier Code I – The reported value is between the laboratory method detection limit 

and the laboratory practical quantitation limit. The results were considered to be accurate 

and are acceptable for use in the analysis. 

Qualifier Code J – The laboratory remark code J indicates the resulting value is an 

estimated value and is not a result of analytical measurements. However, the data was 

considered accurate and acceptable for use in the analysis. 

Qualifier Code U – The laboratory remark code U indicates that no TN or TP 

concentrations were detected in the collected sample. The value was reported as the 

minimum detection limit. The data were included in the TMDL analysis. 

Upon completion of a range test and review of qualifiers, the Client Sample ID was used to 

merge the field and laboratory results. 

FDEP IWR Data 

Using SAS v 9.2, water quality data including TN, TP and specific conductivity were queried 

from the IWR Run 42 database by WBID. All stations identified with an organization code 

of 21FLKWAT (Lakewatch) were removed from the dataset prior to analysis. At this time, 

Lakewatch data are not included as part of the datasets used for the determination of 

impairment status by FDEP. In review of the laboratory data, the following data qualifier 

codes were reported for either TN or TP data used for the analysis: 

Qualifier Code I – The reported value is between the laboratory method detection limit 

and the laboratory practical quantitation limit. The results were considered to be accurate 

and are acceptable for use in the analysis. 

Qualifier Code + - Unknown, The results were considered to be accurate and are 

acceptable for use in the analysis. 

The daily median values for each parameter were calculated to ensure that duplicate 

readings per station by date were not present. The daily medians from the IWR Run 42 

dataset were used to develop the comprehensive database. 

Atkins Comprehensive Database 

The Collier County and IWR data were reviewed to ensure the reporting units were 

consistent for all parameters utilized. If necessary, the appropriate data conversion was 
24

performed to make all results comparable within a parameter. Prior to merging the two 

datasets, data headers were re-labelled for consistency. Field blanks and duplicates were 

not included in the development of the salinity-normalized NNC for Clam Bay. Only those 

stations which had both TN or TP and Specific Conductivity were used to establish the sitespecific Clam Bay salinity-normalized NNC (Table 2). 

Water quality stations used to develop site specific Clam Bay salinity-normalized NNC. 

Station Name Data Source 

CB1 Collier County 

CB2 Collier County 

CB3 Collier County 

CB4 Collier County 

CB5 Collier County 

CB6 Collier County 

CB7 Collier County 

CB8 Collier County 

CB9 Collier County 

21FLFTM EVRGWC0043FTM FDEP IWR Run 42

 Account for all waters listed as impaired in south Florida and how maintaining existing 

conditions is protective. Describe the nearshore keys Reasonable Assurance Plan vs. DEP’s 

proposed criteria.

Attached is a comprehensive summary of the information DEP has compiled as part of the 

Impaired Waters Rule listing process. Specific conclusions regarding each Waterbody 

Identification code segment (WBID) are provided in columns AC and AD. Waterbodies in 

Category 4e are on the EPA 303(d) list, not the state Verified list for nutrients, but FDEP 

has specific reasons (provided below) that EPA should remove these WIBDs from the 

303(d) list. 

The perceived discrepancies between DEP’s healthy existing approach and the fact the 

some areas are listed as impaired can be explained by the following:

 In many cases, the impaired water is a canal, protected bayou, or tidal area that was 

not used for criteria development. DEP nutrient criteria apply only to the actual open 

water estuarine segments as specified in Chapter 62-302. Once a TMDL is established 

for an impaired canal, protected bayou, or tidal area, the TMDL will become the site 

specific interpretation of the nutrient criteria (hierarchy 1 interpretation). During the 

development of the numeric nutrient criteria proposed by DEP, only stations from 

open estuarine areas were included in the statistical derivation, and canals, protected 

bayous, and tidally influenced areas that alternate between fresh and marine waters 

were specifically excluded because they represented a resource distinctly different 

from the remainder of the estuary. Available information indicates it is not 

appropriate to apply numeric nutrient criteria developed for the open water segments 

of estuaries to these canals, bayous, and low/fluctuating salinity tidal areas (see Eyre 
25

1998 and Wolanski et al. 2004). The narrative nutrient criteria (no imbalances of flora 

or fauna) would continue to apply to these important nursery zones.

 The area was listed as impaired for DO with no causative pollutant identified as 

responsible. Waterbodies that do not attain the DO criteria but a causative pollutant 

cannot be identified are place in category 4d, which are on the EPA 303(d) list, but are 

not on the State Verified list. FDEP is in the process of establishing new DO criteria 

that will largely address this DO issue, especially the natural background condition 

provision. With no demonstration that nutrients are related to the DO, FDEP believes 

that DO is irrelevant to nutrient criteria development in these particular waters. As 

described in each estuary document, DEP determined that nutrients were not 

associated with sporadic low DO values in various estuary segments, and that natural 

factors (mangrove leaf litter decomposition, natural sediment oxygen demand, 

natural high temperatures, and stratification) were responsible for the observed low 

DO.

 For the Keys, data from the area within 500 meters from each island were not used for 

the healthy existing conditions approach and instead, the Keys Reasonable Assurance 

Plan provides the reductions needed to achieve applicable nutrient targets for this 

“halo” zone. DEP criteria in Chapter 62-302 apply 500 meters from the island out to 

the spatial extent of each segment depicted in Chapter 62-302. Note that the FL Keys 

Reasonable Assurance (RA) Document was adopted for the Florida Keys since the last 

TMDL assessment cycle (early 2012). FDEP’s evaluation of the biological resources of 

the Florida Keys indicates that the waters in the nearshore zone area (state waters 

beyond 500 m) support a healthy well-balanced community, are attaining the 

designated use, and have not shown adverse effects from nutrient enrichment in the 

nearshore area (beyond 500 m). 

DEP has adopted the criteria established in the FL Keys Reasonable Assurance 

Document, which are based on improving water quality in the inshore halo zone to 

modeled targets. The RA plan will reduce the anthropogenic pollutant loading to 

these WBIDs, and DEP will reassess the area once all restoration activities have been 

completed to determine if the nutrient targets have been achieved. Additionally, the 

nearshore/”canal” WBIDs are also in category 4e for DO, and DEP will reassess the DO 

issue after the RA plan has been implemented.

 For Rookery Bay, the nutrient impairment listing was in error, due to nonrepresentative sampling, and a detailed explanation describing why it should be 

delisted is provided. The listing was primarily based on chlorophyll a data collected 

during 2006 by the FDEP District Office in Fort Myers. However, the data were 

collected as a part of a study targeting isolated nutrient sources such as golf courses, 

wastewater sprayfields, and dead-end canals, and were not representative of the 

general conditions within the bay or WBID. Most of the sites included in this study 

were located in the most inland portions of the WBID, with some of the sites 

appearing to be more fresh water than estuarine or marine. Since the data from this 

targeted study made up a large majority of the data used in the IWR assessment, the 

results of the assessment indicated an annual average chlorophyll a level above the 

threshold for impairment. When the annual average chlorophyll concentration for 

Rookery Bay was recalculated incorporating additional, more representative data 

collected by FIU as part of its extensive south Florida coastal and estuary monitoring 

program, the result is well below the threshold for listing. The FIU data were not used 
26

in the original assessment because FIU did not enter the data into STORET, which is 

the primary data source for the IWR assessments. Therefore, the listing for 

chlorophyll/nutrients in Rookery Bay is s inaccurate and will be corrected in future 

lists.

 Discuss what FIU described as elevated TN and TP in extreme north Biscayne Bay (July 30, 

2010).

The FIU report was simply comparing absolute nutrient values found throughout Biscayne 

Bay and described sites that were in the upper quartile of the distribution. By definition, 

any selected distribution will have some data points in the upper quartile, and one must 

examine the ecological relevance of the data. The FIU report was not meant to infer that 

the sites with “elevated” levels (upper quartile values) were inappropriate for northern 

Biscayne Bay or that existing nutrient levels in any way did not support the designated use 

of the system. 

The width of the bay ranges from 1.6 to 16 km, and its length is approximately 88.5 km, 

extending in a southwesterly direction from Dumfoundling Bay in the north to Barnes 

Sound in the south. The narrow north area has a much lower flushing rate than does the

wide southern portions that are open to and contiguous with the Atlantic Ocean. Note 

that the northern area also has large areas (> 1000 acres) of intact mangrove forest (Oleta 

River State Park and East Greynolds Park) that would naturally contribute TN and TP from 

the decomposing leaf litter. Seagrass (T. testudinum, S. filiforme and H. wrightii)

compose 25% of the bottom in north Biscayne Bay, and there is no light limitation from 

the existing chlorophyll levels. For example, the long term average chlorophyll in 

northern Biscayne Bay is a very low 1.4 ug/L, and more than 20% surface light reaches the 

bottom. Based on the weight of evidence, FDEP concluded that the existing nutrient and 

chlorophyll levels in northern Biscayne Bay were fully protective of a healthy, well 

balanced community.

 Describe how below detect values were used.

Below detect values are substituted with one half the Method Detection Limit (MDL) for 

calculations.

 Provide more explanation of Brecino segmentation, screening, MDLs, outliers, climate, 

exclusions.

Quality Assurance and screening consisted of identifying data points with fatal qualifier 

codes (J, Q, K, N, O, and Y) and excluding such data from the additional analysis. Any 

values reported as less than the method detection limit (MDL) were replaced with 1⁄2 the 

value of the reported MDL.

Florida International University (FIU, Boyer and Briceno) used a holistic approach for basin 

segmentation to account for variability, not only dictated by a given nutrient 

concentration level, but also by a combination of other factors (water clarity, climate, 

weather, extreme events, geomorphology, circulation and exchange, management, etc.). 
27

Basin segmentation was accomplished with an objective classification of station sites 

combining Principal Component Analysis (PCA) and Hierarchical Clustering methods in 

tandem. 

Between 8 and 13 selected biogeochemical variables were used for the PCA for each of 

the six south Florida basins (Biscayne Bay, Florida Bay, Florida Keys, Whitewater Bay10,000 Islands, Gulf Shelf and Pine Island-Rookery Bay). Statistics (mean, standard 

deviation, median and median absolute deviation) of retained scores from PCA were input 

into Hierarchical clustering routines. The rationale behind the selection of these statistics 

was to account not only for the level of individual parameters but also for their variability. 

Then, progressive subdivisions were obtained varying the statistical distance among 

groups. Selection of the final number of segments was based on local knowledge. Spatial 

extension and pattern, geomorphology, water circulation and benthic ecosystem 

distribution played a major role on the decision. In summary, FIU statistically 

characterized and subdivided waters in each basin into what they considered 

biogeochemically and spatially coherent segments.

After discussing with the Marine Technical Advisory Committee, FDEP adopted the FIU 

segmentation approach described above. 

Additional Request for Clarification Received on 8/22/12

1) Please describe the rationale for changing the exceedance frequency for chlorophyll a (20 ug/l 

for streams, and 11 ug/L for estuaries) from not to be exceeded in any year to not to be 

exceeded more than once in three years.

The Department changed the exceedance frequency for the chlorophyll a impairment 

threshold for streams and estuaries from not to be exceeded in any year to not to be 

exceeded more than once in three years because 

a) it makes the thresholds consistent with the expression of the vast majority of newly 

adopted numeric interpretations of the nutrient standards, 

b) during the first ten years of implementation of the IWR, Florida listed many waters for 

nutrient impairment based on single year exceedances of the chlorophyll a threshold that 

were caused by extreme weather conditions (both droughts and El Nino events) rather 

than anthropogenic nutrient loading, and these waters were subsequently delisted when 

there were at least three subsequent years that did not exceed the threshold. Given the 

delisting threshold that delists waters when the listing threshold is not exceeded for three 

consecutive years, the change in exceedance frequency is actually not a significant change 

in the rule. However, this cycling of waters on and off the 303(d) list is administratively 

very inefficient, and the Department wants to ensure that only truly impaired waters are 

listed as such.

c) The requirement that the chlorophyll a threshold not be exceeded in any year means that 

no annual geometric mean can exceed the threshold over the 7.5 year Verified List period 

(i.e., 7 annual average). Although the rule provision allows the annual geometric 

chlorophyll a to go up to 20 μg/L in a stream, the reality is that the long-term average 
28

conditions must be substantially below the threshold in order for a stream to not be 

listed. This is because there is variability around the long-term average, both due to 

natural factors and sampling and testing. 

The binomial distribution can be used to predict the percentile of the annual geometric 

mean distributions at which 20 μg/L must occur in order for a stream WBID never to 

exceed (0 out of 7 years) the threshold. Based on the binomial distribution and 

assumption of inter-annual independence (i.e., no or minimal autocorrelation between 

years), it can be expected with 99.9% confidence that the 99.99th percentile geometric 

mean concentration will not be exceeded in any year out of a 7-year period. In other 

words, it is expected that 20 μg/L would be exceeded in only 0.1% of the years. 

DEP evaluated inter-annual variability in EPA benchmark stream chlorophyll a levels and 

found that inter-annual standard deviation (natural log-transformed) typically ranges from 

0.170 to 0.457. Given this level of variability, the long-term geometric chlorophyll a 

concentration in a stream WBID would need to be between 3.8 and 10.8 μg/L to never 

exceed the chlorophyll a threshold of 20 μg/L with 99.9% certainty. 

It should also be noted that the chlorophyll a nutrient impairment threshold for streams is 

only one of several floral thresholds used to assess streams for attainment of the narrative 

nutrient criterion (in addition to the TN and TP nutrient thresholds), and that EPA’s 

promulgated NNC for streams did not include a chlorophyll a criterion

2) Please explain the discrepancy in the explanation of the reference/benchmark sites used to 

establish the floral metric for the LVS. Page 23 of the SCI Primer refers to 58 sites, with 19 

having sufficient plant growth, while Table A-2 in the implementation document refers to 41 

sites.

The Primer document was making reference to an earlier data set that included both sites that 

were part of EPA’s reference stream list and sites that were determined to be healthy by 

passing the SCI. To be consistent with the EPA methodology used for establishing the actual 

numeric thresholds for TN and TP, DEP chose to include only the EPA reference sites with 

sufficient plant information (41 sites) when establishing the final guidance on the LVI, which 

are presented in Appendix A-2 of the Implementation document.

3) Please provide the rationale for changing the definitions for predominantly marine and 

predominantly fresh (why appropriate to use conductivity, and why we struck “at the surface).

The adopted rule states that “Predominantly marine waters” shall mean surface waters in 

which the chloride concentration is greater than or equal to 1,500 milligrams per liter or 

specific conductance is greater than or equal to 4,580 μmhos/cm. Because there is a well 

known, established relationship between chloride, conductivity, and salinity, and because 

conductivity data are far more available than chloride data (which was formerly required), 

DEP chose to add the equivalent conductivity value as an alternate way to determine the fresh 

versus marine waters distinction. Additionally, because tidal waters commonly have a salinity 

wedge due to the density of salt water, DEP provided the additional option that 

measurements could be taken at the bottom, where the salt wedge is typically present.
29

4) Please provide the page numbers in one of the estuarine reports where the Department 

describes the basis for the 1 in 3 exceedance frequency.

The basis for the 1 in 3 exceedance frequency is described on page 32 of the Biscayne Bay 

report. It is described in more detail on pages 25 and 26 of the NNC Overview Document. 

5) Please explain how the text in subsection 62-303.450(1) of the Impaired Waters Rule related to 

the nutrient assessment for estuaries will be implemented, particularly in regard to the 

assessment of the chlorophyll a threshold for estuaries.

This section incorrectly references subsection 62-303.353(1), when it should have referenced 

subsection 62-303.353(2). Subsection 62-303.450(1), F.A.C., specifically focuses on chlorophyll 

a levels in streams and estuaries, and the Department intended to reference subsection 62-

303.353(2), which assesses estuaries against the long-standing 11 ug/L nutrient impairment 

threshold for estuaries. In contrast, subsection 62-303.353(1) is part of the nutrient 

assessment that places waters on the planning list if they exceed the numeric interpretations 

of the narrative nutrient criterion established in subsection 62-302.531(2), which for estuaries 

would include nutrient TMDLs and the newly adopted estuary-specific numeric interpretations 

in Rule 62-302.532, F.A.C. These estuary-specific numeric interpretations, which establish 

independently applicable TN, TP, and chlorophyll a criteria for estuaries from Tampa Bay to 

Miami and the Florida Keys, are assessed under Subsection 62-303.450(3). In fact, subsection 

62-303.450(3) also references subsection 62-302.353(1), and this redundant rule citation 

further supports the fact that we inadvertently referenced the wrong rule in 62-303.450(1). 

The Department plans to correct the rule reference as part of the ongoing Triennial Review of 

Florida’s Water Quality Standards, which we currently plan to take before the ERC in 

December. We also plan to clarify that the 11 ug/L chlorophyll nutrient impairment threshold 

will not be assessed in estuaries with estuary-specific chlorophyll a criteria. This is consistent 

with the hierarchy in Rule 62-302.531, (2), F.A.C., which establishes site specific numeric 

interpretations of the narrative nutrient criterion as the primary interpretation of the 

narrative nutrient criterion.

6) Please add the decision matrix for the stream assessment into the implementation document

This has been added.

7) Please explain the assessment process for cases where the Department believes that 

exceedances of the DO criteria are due to natural conditions [revisions to Rule 62-

303.420(1)(b)].

While there were several changes to this existing rule provision, the Department would like to 

not that the changes were only indirectly related to the revisions to Florida’s nutrient 

standards. The most substantive change to this section was to limit its application to 

Dissolved Oxygen (DO), while it previously applied to other parameters. The revisions also 

changed references to “bioassessments” to “Biological Health Assessments,” which is the 

new, more specific term used in the nutrient standards revisions, and clarified language about 
30

where the BHA information needed to be collected relative to water quality samples were 

taken. The revisions also deleted text about the concentrations of TN, TP, and BOD in the 

waterbody “relative to comparable reference waters.” While this text was deleted, the 

Department still plans to document for the record the basis for its conclusion that the DO 

exceedances are due to natural background conditions, and this demonstration will include 

comparison of the waterbody’s nutrient and BOD levels to reference conditions and 

evaluation of potential anthropogenic sources of nutrients or BOD in the watershed.

8) Please explain why the schedule for estuarine NNC development in Rule 62-302.532(3), F.A.C., 

only mentions criteria for TN and TP, and note whether the Department intends to also address 

chlorophyll a.

The Department only listed TN and TP in this rule provision based on our understanding of 

EPA’s January 14, 2009 determination that numeric nutrient criteria were necessary to meet 

the requirements of the CWA, which does not require criteria for response variables. This 

understanding was further reinforced by EPA’s promulgation of stream criteria that did not 

include a response variable. Notwithstanding this interpretation, the Department plans to 

adopt chlorophyll a criteria as part of the nutrient criteria for Florida’s estuaries. 

9) Please provide documentation that the halozone is not included in the area where the Keys NNC 

apply. 

Additional explanation has been given above.
31

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Burlington, New Jersey. Chesapeake Science 18:253-265. 

Dame, R., D. Bushek, D. Allen, D. Edwards, L. Gregory, A. Lewitus, S. Crawford, E. Koeppler, 

C. Corbitt, B. Kjerfve, and T. Prins. 2000. The experimental analysis of tidal creeks 

dominated by oyster reefs: the premanipulation year. Journal of Shellfish Research, 19 (1): 

361-369.

Day, J.W., Jr., C.A.S. Hall, W.M. Kemp and A. Ynez-Arancibia. 1989. Estuarine Ecology. John 

Wiley and Sons, New York, NY. 

Diaz, R.J. 1989. Pollution and tidal benthic communities of the James River Estuary, Virginia. 

Hydrobiologia 180:195-211. 

Diaz, R.J. and L.C. Schaffer. 1990. The functional role of estuarine benthos. Pp. 25-56 in: 

Perspectives on the Chesapeake Bay, 1990. Advances in estuarine sciences. M. Haires and 

E.C. Krome, eds. Chesapeake Research Consortium, Gloucester Pt., VA. Rpt. No. 

CBP/TRS41/90 

Eyre, B. 1998. Transport, retention and transformation of material in Australian estuaries. 

Estuaries 21:540-551. 

Fain, A.M., D.A. Jay, D.J. Wilson, P.M. Orton and A.M. Baptista 2001. Seasonal and tidal 

monthly patterns of particulate matter dynamics in the Columbia River estuary. Estuaries 

24:770-786. 

FDEP. 2010. Overview of Approaches for Numeric Nutrient Criteria Development in Marine 

Waters. Florida Dept. Environmental Protection. 98 pp.

Fisher, T.R., L.W. Harding, D.W. Stanley and L.G. Ward. 1988. Phytoplankton, nutrients, and 

turbidity in the Chesapeake, Delaware, and Hudson estuaries. Estuarine, Coastal and Shelf 

Science 27:61-93.

Gilmore, R.G. 2007. Early life history of sciaenid fishes: emphasis on the sand seatrout in the 

St. Lucie estuary. Final Report to SFWMD, West Palm Beach, FL. 

Gunter, G. 1945. Studies on Marine Fishes of Texas. Publications of the Institute of Marine 

Science, University of Texas 1:1-190. 

Gunter, G. 1961. Some relations of estuarine organisms to salinity. Limnol. Oceanogr. 6:182-

190. 
32

Holmes, R.M., B.J. Peterson, L.A. Deegan, J.E. Hughes and B. Fry. 2000. Nitrogen 

biogeochemistry in the oligohaline zone of a New England estuary. Ecology 81:416-432. 

Hughes, J.E., L.A. Deegan, B.J. Peterson, R.M. Holmes and B. Fry. 2000. Nitrogen flow 

through the food web in the oligohaline zone of a New England estuary. Ecology 81:433-452. 

Janicki. 2011. Sarasota Bay Numeric Nutrient Criteria: Tidal Creeks, Letter Memorandum to 

Sarasota Bay Estuary Program. 12 pp.

Jassby A.D., W.J. Kimmerer, S.G. Monismith, C. Armor, J.E. Cloern, T.M. Powell, J.R. Schubel 

and T.J. Vendlinski. 1995. Isohaline position as a habitat indicator for estuarine populations. 

Ecological Application 5:272-289. 

Jones, K.K., C.A. Simenstad, D.L. Higley and D.L. Bottom. 1990. Community structure, 

distribution, and standing stock of benthos, epibenthos, and plankton in the Columbia River 

Estuary. Progress in Oceanography 25:211-241. 

Kimmerer, W.J. 2002. Physical, biological, and management responses to variable 

freshwater flow into the San Francisco estuary. Estuaries 25:1275-1290. 

Leppakoski, E. 1975. Assessment of degree of pollution on the basis of macrozoobenthos in 

marine and brackish water environments. Acta Academiae Aboensis, Ser B 25:1-90. 

Lin, J. and A.Y. Kuo. 2003. A model study of turbidity maxima in the York River estuary, 

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