### 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

e nsure 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 co nsumption, recreation and the propagation of fish and wildlife are protected.

DEP addressed this in detail in the TSD ( p. 161 ) and recommended P roposed Final O rder ( 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

.

 F or 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
nutrient s 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
C entral, high phosphorus region of the state (see below). After more closely exami ning 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 v er s us 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 provide d in the TSD ( p.86 ) and additional information is presented below for the main areas

.

### 3 Sarasota Area

T he “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 Saraso ta 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 pr esent 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 an d West Central Regions (Figure 4 ). Applying the Peninsular to tal 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 wh ich 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 ar e 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 influ enced 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 i n the TSD ( p.133 )
, the SCI Primer ( Section 2.7 ), and the NNC Implementation Document ( p. 6 )

.

 F or 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 )

.

 F or 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 ar e poor correlations between nutrients and all biological response variables (both floral and faunal) because there are multiple confounding factors affecting the expression of nut r ients

. 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 communit y , then
it can be conclud ed that the stream is healthy, and that nu trients 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 b e healthy via the SCI.

DEP would like to see s pecific examples of w aterbodies that have been listed as impaired but with passing SCI scores. None were i dentified d uring 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.

 F or 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 tha t 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 c riteria (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)

.

### 9

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

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

NEP E stuaries

 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 Tec hnical 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 Saraso ta Bay). For Charlotte Harbor , the estuarine system was divide d into 14 estuarine segments with differing water quality and distinctive resource management con di tions ( s ee 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 underst ood 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 divers ity 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 th is “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 ea ch 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 anthro pogenic 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 scienti

fic 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 de

pth 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 restor ing the system, including a demonstration of the bases for the nutrient targets.

Each individual e s tuary r eports contains the details of the weight of evidence approach used by the Department to ensure that balanced natural populations of aquatic flora an d 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 i ndividual Estuary Reports.

 F or 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 Environmenta l

. Mr

. Janicki explained that in each system, there were different

amount s of data available, which influence d 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,

co mplex 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 m atter) 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 cr iteria 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 distinct ly different from the remainder of the estuary. Available information indicates it is not appropriate to apply numeric nutrient criteria developed for the open water segm ents of estuaries to these low/fluctuating salinity tidal areas (see Eyre 1998 and Wo lanski 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 wat er 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 h igh 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 estuarie s 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 prod uction (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 Schaff ner 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 wa ter 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, 200 3, 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 an adromous 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 f reshwater 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, Chesa peake 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 sa linity 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 sou rces 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 su spended 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 hab itat 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 de veloped 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
Flori da 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).

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 t he downstream, open water estuary (Figure 9).

Figure 9. Phosphorus and chlorophyll a levels by land use class and longitudinal gradien t in selected southeast US estua ries. 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 pro ductivity). 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 (Janick i, 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) remai ns appropriate for

### 16 these areas

. Literature references for the discussion on salinity zones are provided in Attachment A.

 F or 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 Ba y

See section 2.2 of the Sarasota Bay TSD, which describes how the relationship between nutrients and chlorophyll a in th e Sarasota Bay segment is influ enced by color , which in turn is related to swamp inputs.

 F or 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 G ary 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 lim it 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 b oundaries 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 T ype 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 f reshwater 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 th e 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, s ee 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://ser c.fiu.edu/wqmnetwork/SFWMD

CD/index.htm . DEP downloaded the entire FIU data set directly from the website. Da ta 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 in itiated 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 detec tion 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 ap proach” was described in i ndividual r eports ( see PFO, p.53

- 69 for a summary).

All

 Provide an explanation h ow 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 Q uestions 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 WBID s 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 condu cted and how it would help with downstream protection.

An example invo lv ing the Weeki Wach i River was i nserted 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 concen trations 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 chlorophy ll 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 scientific ally 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 condit ions 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 wa terbodies, 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, s ediment 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., E stero 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 w ere 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 sam ples, it should be noted that t he annual geometric mean TN and TP values for Clam Bay are within the range of average values observed at other healthy

estua ries 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 ass urance.

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

w ater 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 retrie ving 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 month ly 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 M onitoring 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 an d 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 laborator y 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 manufacture r 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 complet e

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, blin d 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 Colli er 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 we re 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 concen tration 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 w ere 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 accepta ble 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 analys is.

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 rev iew 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 l imit. 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 wer e 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 reviewe d 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 site

specific Clam Bay salinity

- nor malized 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 W ater b ody Id entif i cation 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, th e 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 atta in 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 S tate 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 docume nt, 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 m eters from each island w ere not used for the healthy existing conditions approach and instead, the Key s Reasonable Assurance Plan provides the reductions needed to achieve applicable nutrient targets for this “halo” zone. DEP criteria in Chapter 62

- 302 apply 500 m eters 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 f or 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 comm unity, 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 improvin g 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 target s 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 R ookery Bay , the nutrient impairment listing was in error, due to non

representa tive 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 mo st 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 indica ted 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 mo nitoring 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 f or 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 fo und 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 portion s 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 chloroph yll 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 detecti on 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, clim ate, 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 metho ds in tandem.

Between 8 and 13 sel ected biogeochemical variables were used for the PCA for each of the six south Florida basins (Biscayne Bay, Florida Bay, Florida Keys, Whitewater Bay

10,000 Islands, Gulf She lf 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 paramet er s 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 circ ulation 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 wit h 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 inter pretations 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 condi tions (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 w aters 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, t his cycling of waters on and off the 303(d) list is administratively very ineffici ent, 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 Veri fied 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 distributi ons 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 expe cted 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

- an nual 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
concentrati on 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 di screpancy 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 4 1
sites.

The Primer document was making reference to an earlier data set that i ncluded 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 Im plementation 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 t here is a well know n , 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

v ersus marin e 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 descri bed 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 t he 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 le vels 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 estua ry
- 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 asse ssed 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 plan s 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 threshol d 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 p rimary 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 rela ted 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 Dep artment still plans to document for the record the bas is 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 , whic h 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 chlorophyl l 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 Appendix A: Salinity Zone Literature Cited

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- 406.

Crumbs, S.E. 1977. Macrobenthos of the tidal Delaware River between Trenton and 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
Wi ley 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 estuari es. 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 f or 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 estuar ies. 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. Ec ology 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. Vendl inski. 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, epibentho s, 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. 197 5. 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, Virginia. Estu aries and Coasts 26:1269

- 1280.

Loneragan N.R. and S.E. Bunn. 1999. River flows and estuarine ecosystems: Implications for coastal fisheries from a review and case study of the Logan River, Southeast Queensland. Australian Journal of Ecology 24: 431

- 440

M assmann, W.H. 1954. Marine fishes in fresh and brackish waters of Virginia rivers. Ecology
35:75

- 78.

Montagna, P.A. and Kalke, R.D. 1992. The effect of freshwater inflow on meiofaunal and macrofaunal populations in the Guadalupe and Nueces Estuaries, Texa s. Estuaries 15:307

- 326.

North, E. W., R. R. Houde, S. Y. Chao, and L. P. Sanford. 2005. The influence of episodic events on transport of striped bass eggs to the estuarine turbidity maximum nursery area.
Estuaries 28:108

- 123.

North, E.W. and E.D. Houde. 2001. Retention of white perch and striped bass larvae: Biological

- physical interactions in Chesapeake Bay estuarine turbidity maximum. Estuaries
24:756

- 769.

### 33 North, E.W. and E.D. Houde. 2003. Linking ETM physics, zooplankton prey, and fish early

- life his tories to striped bass Morone saxatilis and white perch M. americana recruitment. Marine Ecology Progress Series 260:219

- 236.

Odum, W. E., L. P. Rozas, and C. C. McIvor. 1988. A comparison of fish and invertebrate community composition in tidal freshwater and oligohaline marsh system. Pp. 561

- 569. In Hook, D. D. et al (Eds.) The Ecology and Management of Wetlands, Volume I: Ecolo gy of Wetlands. Timber Press, Portland, Oregon.

Odum, W. E., T. J. Smith III, J. K. Hoover, and C. C. McIvor. 1984. The ecology of tidal freshwater marshes of the United States east coast: a community profile. U. S. Fish and Wildlife Service FWS/OBS

- 83/17 . 177 p

Peterson, M.S. and S.T. Ross. 1991. Dynamics of littoral fishes and decapods along a coastal
river

- estuarine gradient. Estuarine, Coastal and Shelf Science 33:467

- 483.

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