# CHAPTER 2 Issue Category: Technical Support Document Pages 4698-4773

Response to Public Comments Water Quality Standards for the State of Florida's Lakes and Flowing Waters

November 14, 2010

40 CFR Part 131 Docket #: EPA-HQ-OW-2009-0596

This document is part of a larger documentChapter 2 - Comment Documents Technical Support Document 

# TSD - TECHNICAL SUPPORT DOCUMENT No Comments are Applicable to this Issue Category, and Thus No Response is Necessary.


# CHAP1 - CHAPTER 1: LAKES Comment ID 1355-2.001.014
Author Name: Barker V. Organization: Brevard County Board of County Commissioners

- There are several inaccurate statements in the description of what a regression line and prediction interval is in the TSD and the rule. It is stated that "the regression line and equation define the average relationship (i.e., half the points fall above the line and half below it)." This statement is not accurate. While the regression line can be thought of as the mean response given a value of x, it is not true that it separates the data into two even groups. 

# Response
Comment ID: 1355-2.001.014 Response: EPA agrees with the commenter regarding descriptions of the regression line that "half the points fall above the line and half below it" is incorrect. EPA has clarified in its descriptions of regression lines, where applicable, what they indicate in the final TSD. 

# CHAP1A - 1A. METHODOLOGY FOR PROPOSED LAKE CLASSIFICATION Comment ID 0896-1.001.002
Author Name: * * Organization: Lee County Division of Natural Resources Chapter 1. Methodology for Proposed Lake Classification In general, the method is not consistent with the watershed approach employed for streams. By comparison the watershed approach was employed and more consistent when evaluating streams and estuaries, considered ecological responses and geology more directly than the lake system evaluation.

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# Comment ID 0896-1.001.003
Author Name: * * Organization: Lee County Division of Natural Resources Chapter 1. Methodology for Proposed Lake Classification, i. Background Page: 1-2 Alkalinity is not always a good indicator of the underlying geology that would affect nutrient cycling. The methodology on flowing waters (streams/canals) considers geology more extensively. It would be useful to use a method consistent with that of the stream/canal evaluation method rather than assuming alkalinity is an adequate surrogate for geology in lakes. 

# Comment ID 0896-1.001.004
Author Name: * * Organization: Lee County Division of Natural Resources Chapter 1. Methodology for Proposed Lake Classification, v. Color, Alkalinity & Specific Conductance Page: 1-3 Lake color varies based on naturally occurring physical and chemical events. Large inputs to a lake system can have long impacts on the color, alkalinity and conductance. A gradient associated with differentiating "colored" versus "clear" systems or a gradient associating pH and nutrients may be a more realistic depiction of systems given that they have a range of frequency, duration and magnitude nutrient impact before exhibiting a systemic response and anthropogenic impacts can affect all of these parameters. 

# Comment ID 0974.001.008
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago The following are the comments on Chapter 1 : Methodology for Deriving EPA's Proposed Criteria for Lakes of Technical Supporting Document (TSD) for EPA's Proposed Numeric Nutrient Criteria for Florida Inland Surface Fresh Waters. 1 . The District agrees in general with the methodology that EPA utilized to develop numeric nutrient criteria for the inland Florida lakes from classifying lakes into different types, establishing chlorophyll a thresholds referencing various approaches, and deriving numeric nutrient criteria based on the relationship between nutrients and chlorophyll a concentrations .

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# Comment ID 0974.001.020
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago The same approach should be considered for the lakes, as there is strong evidence that the relationship between chlorophyll a and TP and TN varied significantly region by region, as shown in Figures 1-9 and 1-10 on pages 1-30 and 1-31 of TSD. The District suggests that numeric nutrient criteria for the lakes in Florida be derived based on nutrient watersheds and lake types. 

# Comment ID 1476-2.001.041
Author Name: Wehle C. Organization: South Florida Water Management District Page 2 "Nutrient concentrations, chlorophyll concentration, specific conductance, and alkalinity were log-transformed (natural log) for statistical analyses." Please clarify that the transformations were for raw data. Why was natural log used? Were other transformations considered? How was it determined that transformations were needed? 

# Comment ID 1476-2.001.042
Author Name: Wehle C. Organization: South Florida Water Management District Page 2 "FDEP categorized lakes into clear and colored lakes on the basis of the geometric mean color for the period of record." This is not consistent with the footnote statement on Table 1-4 "Platinum Cobalt Units (PCU) assessed as true color free from turbidity. Long-term average color based on a rolling average of up to seven years using all available lake color data." 

# Comment ID 1476-2.001.043
Author Name: Wehle C. Organization: South Florida Water Management District Page 2 How were shifts between colored and clear classification of some lakes (including Lake Okeechobee) handled?

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# Response
Comment ID: 1476-2.001.042 Response: EPA’s analysis and model development of statewide lake data used annual geometric means of alkalinity, color, chlorophyll, TN and TP; with a requirement for at least 4 observations for chl-a, TN, and TP in 2 seasons (no minimum data requirements for alkalinity or color). For missing alkalinity data in the FDEP data set, EPA used alkalinity observations from the IWR data set (primarily Florida Lakewatch data). Lakes were categorized into alkalinity and color classes using geometric means of color and alkalinity for the period of record.

Comment IDs: 0896-1.001.002, 0896-1.001.003, 0896-1.001.004, 0974.001.020, 1476-2.001.043, 0974.001.008 Response: EPA disagrees with comments suggesting lake criteria should be derived based on a watershed approach. EPA also disagrees with commenters who suggested alkalinity is not an appropriate factor upon which numeric nutrient criteria are derived. EPA derived criteria based on the abiotic factors that have the strongest influence on the ambient nutrients and the biological responses to nutrients in lakes, specifically alkalinity and color, and EPA agrees with commenters who suggested this approach. EPA’s analysis supports this conclusion (see final rule TSD). EPA also points out that FDEP’s draft lake criteria (FDEP 2009) were also based on the same conclusions regarding alkalinity and color. EPA acknowledges the influence of watersheds on lake nutrient dynamics and biological responses to nutrients. Lakes are clearly influenced by the streams that flow into them. As such, EPA is finalizing a regulation that will provide protection in the watershed context. EPA refers commenters to the final rule language and preamble discussion regarding downstream protection of lakes. With respect to potential color shifts in lakes over time, EPA has specified that the long-term color for a lake be used as the basis for determining the appropriate lake class and respective criteria applicable. EPA re-examined FDEP data with respect to lake alkalinity. Alkalinity of Florida lakes ranges from near zero (acidic lakes with no ability to neutralize acid) to well over 200 mg/L as CaCO3. The distribution of alkalinity reveals a mode near 50 mg/L, with a long tail of low alkalinity lakes < 20 mg/L total alkalinity. Please see the TSD for details. TP, TN, chl-a, and conductivity are all correlated with alkalinity in the lake data set. Associations of chlorophyll and TN with alkalinity were the strongest, such that low alkalinity lakes were associated with low values of TN and chlorophyll (see final rule TSD). Change-point analysis showed change points in nutrients and chlorophyll in a range of alkalinities of 13-24 mg/L. Since chl-a concentration is the principal lake response of concern, the alkalinity breakpoint could be set at 20 mg/L to reflect similar breakpoints in chl-a and nutrient concentrations. The relation of color to chl-a could be modeled with a quadratic term (see final rule TSD). Nutrient and chl-a concentrations increase with color to a maximum at approximately 50 PCU, and decline above 50. At very high color, light attenuation limits algal growth. References: Florida Department of Environmental Protection (FDEP). 2009. Technical Support Document: Development of Numeric Nutrient Criteria for Florida Lakes and Streams. Florida Department of Environmental Protection, Tallahassee, FL. 173 pp. June 2009. < http://www.dep.state.fl.us/water/wqssp/nutrients/docs/tsd_nutrient_crit.docx >. Accessed September 6, 2010.

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Comment ID: 0974.001.008 Response: EPA appreciates the comments supporting EPA’s approach described at proposal regarding the Agency’s approach to classifying lakes, establishing chl-a thresholds, and deriving criteria based on the relationship between nutrients and chl-a. EPA notes that that the final rule reflects the same general approach described at proposal and supported by the commenter.

Comment ID: 1476-2.001.041 Response: EPA clarifies the purpose of log transformation of nutrient data. Log transformation is not just a matter of statistical convenience, but rather an appropriate method to better organize data for additional analysis. Many fundamental distributions and relationships in nature are power functions: scaling of metabolic rates, energy distributions of molecules in a gas or liquid, chemical rates of reaction, diffusion, size distribution of particles, exponential population growth, and others. For some of these, quantities less than zero are non-sensical (e.g., negative concentrations, negative energy). The most appropriate and general transformation for quantities of field parameters (e.g., concentrations, abundance) is a logarithmic transformation, although others such as inverse or inverse square root are also possible. The root of the log transform is immaterial; EPA selected natural log to maintain consistency with FDEP’s exclusive use of natural log. EPA tested the normality of the log-transformed variables TP, TN, and chl-a. Normal probability plots showed a straight line with deviations from normality at the lower and upper ends (see final rule TSD). Deviations at small values are most likely due to detection limits, and the deviations at high values may be due to truncation of extreme values unlikely to occur in real lakes.Statistical tests of normality of the transformed data (chi-square, K-S, Shapiro-Wilk) all revealed statistically significant nonnormality due to the ends of the distributions. This is a typical example where a large sample size results in statistical significance, but the effect of the non-normal distribution is of no practical significance; it is negligible because the sample size (N) was large( N=1340 for annual means; N > 5000 for individual observations), and also because outliers affected the tests. In particular, there were clusters of detection limit observations for TP and chl-a at the low end of the detection range. At the highest chl-a concentrations, extreme values were less frequent than expected, possibly due to physical constraints (e.g., light limitation) on chl-a concentration (see final rule TSD). Regression is robust to minor deviations from normality (e.g., Zar 1996). Zar, J.H. 1996. Biostatistical Analysis. Third Edition. Prentice-Hall. 

# CHAP1B - 1B. METHODOLOGY FOR PROPOSED CHLOROPHYLL A CRITERIA Comment ID 1355-2.001.020
Author Name: Barker V. Organization: Brevard County Board of County Commissioners They also concluded that there were no seasonal differences in chlorophyll a distributions in lakes based on seasonal box plots provided in Figure 1-3 of the TSD. However, these plots are plotted on a logarithmic scale making them

11/19/2010 02:48 PM EST 2-4702Chapter 2 - Comment Documents Technical Support Document extremely difficult to interpret. Examination of the plots for colored lakes reveals that the median value in summer appears to be twice that of the remainder of the year. Summary statistics and a statistical test should be used to evaluate these differences rather than merely a plot of the data especially when the response axis is compressed by plotting on a logarithmic scale. 

# Comment ID 1355-2.001.030
Author Name: Barker V. Organization: Brevard County Board of County Commissioners As shown if the CART analysis in the TSD, under prediction of chlorophyll was significant at color values between 40-76 PtCo units. Alternatively, lakes with color greater than 76 ug/L may be over-protected since their typical color values reduce penetration of light. Of course, this all assumes EPA methodology is unbiased, which it is not. In establishing criteria for acidic lakes, EPA has departed from the methodology used to develop the chlorophyll a thresholds for alkaline lakes without adequate justification for doing so. It recommended for consistency that the same methodology accepted for alkaline lakes be used for acidic lakes. Therefore, EPA should accept the chlorophyll threshold value of 9 ug/L in establishing the nutrient criteria for clear acidic lakes. 

# Comment ID 1431-1.001.013
Author Name: Levy K. Organization: Pinellas County Department of Environmental Management, Watershed Management Division As part of an argument for using chlorophyll a (and trophic state indices) as a means to evaluate lake condition, the Technical Support Document notes that "maintaining water column chlorophyll concentrations within traditional oligotrophic or mesotrophic limits reduces the risk that submerged vegetation and system functions will be unacceptably altered." While this is true, it should be explicitly acknowledged that some systems naturally exhibit water column chlorophyll a concentrations within the traditional eutrophic range. These types of systems would then require a SSAC placing the burden of correcting an overly protective standard onto the public. Pinellas County recommends that EPA develop region-specific management targets for chlorophyll a using a combination of lake ecoregion and paleolimnological information (Bachmann et al, 2010). 

# Comment ID 1474-1.001.083
Author Name: Herz W. Organization: The Fertilizer Institute The USEPA Technical Support Document for this rulemaking is replete with data showing that the lake responses to nutrient levels vary dramatically for identical nutrient concentrations. See Technical Support Document for U.S. EPA's Proposed Rule for Numeric Nutrient Criteria for Florida's Inland Surface Fresh Waters (hereinafter TSD). Figures 1-1, 1­

11/19/2010 02:48 PM EST 2-4703Chapter 2 - Comment Documents Technical Support Document 9, 1-32 show that for a given TP concentration, chlorophyll a levels may vary by a factor of 30. Figures 1-2,1-10, 1-32 show the same for TN levels. This degree of response encompasses lakes considered unimpaired to significantly impaired and demonstrates that nutrient level is not a reliable indicator of potential impairment. 

# Comment ID 1476-2.001.044
Author Name: Wehle C. Organization: South Florida Water Management District Page 2 "Lakes showed similar chl. a responses regardless of location, with some differences in the range of nutrient concentrations (Figures 1-1 and 1-2)." Please show analysis of covariance to justify the statement. It appears that some of the lake sets have different slopes or are significantly separated to justify sub-setting based on location. 

# Comment ID 1476-2.001.045
Author Name: Wehle C. Organization: South Florida Water Management District Page 4 Salas and Martino (1991) do not discuss Trophic State Indices (TSIs). The citation is inappropriate here. The District suggests the following Kratzer & Brezonik (1981), Brezonik (1984), Dierberg et al. (1988). Page 5 Salas & Martino (1991) did not consider trophic state indices. They considered trophic states based on total phosphorus concentrations. 

# Comment ID 1476-2.001.046
Author Name: Wehle C. Organization: South Florida Water Management District Page 5 Havens (2000) did not suggest averaging the TSIs, rather he suggested looking at differences to define the general mechanism that is maintaining the TSI at the given level. A better citation for this procedure is Carlson & Havens (2005). 

# Comment ID 1476-2.001.047

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Author Name: Wehle C. Organization: South Florida Water Management District Page 5 Salas and Martino considered that same range of TSI values to be mesotrophic in warm-water lakes." Salas and Martino (1991) did not consider TSI values, but rather TP concentrations. 

# Comment ID 1476-2.001.048
Author Name: Wehle C. Organization: South Florida Water Management District Page 12 For designated uses, USEPA should consider Bachmann et al. (1996). 

# Comment ID 1476-2.001.049
Author Name: Wehle C. Organization: South Florida Water Management District Page 13 "The USEPA proposes the TAC suggested nutrient thresholds in clear, high-specific conductance lakes be based on preventing the annual average chl. a from exceeding 20 ug/L." Please clarify: Is this proposal for high (> 100 uS/cm) conductivity, or are you including these in high alkalinity lakes ( > 50 mg CaCO3/L or conductivity > 250 uS/cm). How are lakes with conductivity between 100 and 250 uS/cm and alkalinity < 50 mg CaCO3/L considered? 

# Comment ID 1476-2.001.059
Author Name: Wehle C. Organization: South Florida Water Management District Page 22 Table 1-1. Only the TP values are from Salas and Martino (1991) 

# Comment ID 1836.001.015
Author Name: Moore D.

11/19/2010 02:48 PM EST 2-4705Chapter 2 - Comment Documents Technical Support Document Organization: Southwest Florida Water Management District 5. USEPA chlorophyll a targets that were developed based on oligotrophiclmesotrophic limits are inappropriate for lakes that are naturally higher in nutrients. As part of an argument for using chlorophyll a (and trophic state indices) as a means to evaluate lake condition, the Technical Support Document notes that "maintaining water column chlorophyll concentrations within traditional oligotrophic or mesotrophic limits reduces the risk that submerged vegetation and system functions will be unacceptably altered" (page 1-7, Technical Support Document) . While this is true, it should be explicitly acknowledged that some systems naturally exhibit water column chlorophyll a concentrations within the "traditional" eutrophic range as exemplified by Lake Francis, Highlands County, Florida . Paleolimnological data from Lake Francis indicate that the basin has been historically mesotrophic to eutrophic, and suggest that efforts to limit anthropogenic nutrient loading will not reduce lake nutrient concentrations (Brenner et al. 1993).Another study entitled "Paleolimnological Characterization of Pre-Disturbance Water Quality Conditions in USEPADefined Lake Regions" (Whitmore and Brenner 2002) used regression models developed from sediment core data to estimate historical water quality conditions in eight Florida lakes, including Lakes Shipp, Lulu, Conine, Haines, and May in the WHCL . The results indicated that estimated historical chlorophyll a concentrations in several of the lakes were higher than USEPA's proposed criteria . In a follow up study in 2005, Reidinger- Whitmore et al . used an analogous approach to infer similar historical chlorophyll a values in comparison to Whitmore and Brenner's study . Because there is a multitude of evidence suggesting that regional variability in the interaction between nutrients and chlorophyll a exists, SWFWMD recommends that USEPA develop region-specific management targets for chlorophyll a using a combination of lake ecoregion and paleolimnological information. 

# Comment ID 1836.001.016
Author Name: Moore D. Organization: Southwest Florida Water Management District 6. Proposed criteria requiring the lowering of total nitrogen and total phosphorus levels in lakes that are already meeting chlorophyll a standards are unnecessary. The "weight of evidence" approach used by USEPA for establishing the recommended chlorophyll a criterion seems reasonable (page 1-12, Technical Support Document). Under circumstances where total nitrogen (TN) or total phosphorus (TP) concentrations exceed the proposed standard and chlorophyll a concentrations meet the standard, modified criteria based on 50% prediction intervals are to be used for the TN and/or TP criteria (page 4184, proposed rule) . This approach may occasionally lead to excessively restrictive nutrient criteria in lakes with appropriate chlorophyll concentrations, resulting in avoidable expenditures of management resources to unnecessarily lower nutrient levels. 

# Response Comment IDs: 1476-2.001.045, 1476-2.001.046, 1476-2.001.047, 1476-2.001.059 Response: EPA thanks commenters for suggestions that would make minor corrections to the TSD. EPA has considered these comments and has incorporated many of the suggested corrections in preparing the final rule TSD. EPA may not have incorporated

11/19/2010 02:48 PM EST 2-4706Chapter 2 - Comment Documents Technical Support Document some of the suggested corrections if the citation was not relevant to EPA’s basis for numeric nutrient criteria derivation for Florida’s lakes.

Comment IDs: 1431-1.001.013, 1836.001.015 Response: EPA agrees with the commenters who assert that naturally eutrophic lakes may occur in Florida. However, the fact that a lake is naturally eutrophic does not mean that it has not eutrophied further as a result of human activities. EPA points out that the soil and groundwater conditions that cause natural eutrophy in lakes are the same conditions that promote agriculture and development: rich, alkaline soils are favored for agriculture and consequently the development of settlements, towns and cities; and phosphate deposits are mined for the phosphate rock and gravel in central and north-central Florida. These activities (agriculture, urban construction, mining) promote runoff and erosion, which can carry more of the phosphate to receiving waters than they would have received with only natural vegetation cover. EPA disagrees with commenters who suggest that EPA should manage Florida’s lakes to existing eutrophic conditions. While EPA agrees that many of Florida lakes currently range in trophic state from oligotrophy to hypereutrophy, EPA notes that FDEP judged that the appropriate trophic state consistent with the designated uses and existing narrative criteria for nutrients for Florida lakes is the boundary between mesotrophy and eutrophy (FDEP 2009).Nonetheless, EPA notes that investigations of sedimented diatoms in Florida lakes (Whitmore and Brenner 2002; RiedingerWhitmore et al. 2005) indicate that naturally eutrophic lakes do occur in Florida. Of 32 lakes in Whitmore and Brenner (2002) where pre-1900 TP concentrations had been inferred, 9 lakes were eutrophic (inferred TP > 50 ug/L). In 5 of the 9 historically eutrophic lakes, the inferred TP increased further by more than 25% from the pre-1900 period to the present. The remaining 4 lakes showed no apparent change (< 25% increase or decrease) in TP during the period. EPA’s analysis of paleo-ecological data compiled by Whitmore and Brenner (2002) showed that nearly 60% of the 32 lakes examined had increased in TP concentration.See EPA’s analysis of the paleolimnological data in the final rule TSD. In a second study (Riedinger-Whitmore et al. 2005), bluegreen algae (Cyanobacteria) were found to have increased in inferred abundance in 5 of 6 lakes studied for cyanobacterial pigments. These results suggest that no blanket statement on historic trophic states of Florida lakes can be taken as true, but that all cases of suspected natural eutrophic conditions must be examined with site-specific evidence. Claims that present-day TP concentrations in Florida lakes are natural are not supported by the paleolimnological findings. Based on this analysis, as well FDEP’s rationale for its draft criteria for lakes (FDEP 2009), EPA concluded that managing Florida’s lakes to eutrophy is not an appropriate water quality expectation. Rather, eutrophy is a trophic state that should be prevented unless there is clear evidence to demonstrate that such a trophic state is indeed the natural trophic state for that lake. In such cases, site-specific alternative criteria can be pursued.
References: Florida Department of Environmental Protection (FDEP). 2009. Technical Support Document: Development of Numeric Nutrient Criteria for Florida Lakes and Streams. Florida Department of Environmental Protection, Tallahassee, FL. 173 pp. June 2009. < http://www.dep.state.fl.us/water/wqssp/nutrients/docs/tsd_nutrient_crit.docx >. Accessed September 6, 2010. Riedinger-Whitmore, M., T. Whitmore, J. Smoak, M. Brenner, A. Moore, J. Curtis, and C.L. Schelske. (2005). Cyanobacterial

11/19/2010 02:48 PM EST 2-4707Chapter 2 - Comment Documents Technical Support Document proliferation is a recent response to eutrophication in many Florida lakes: A paleolimnological assessment. Lake and Reservoir Management, 21, 423-435. Whitmore, T. and M. Brenner. 2002. Paleologic Characterization of Pre-disturbance Water Quality Conditions in EPA Defined Florida Lake Regions. University of Florida, Department of Fisheries and Aquatic Sciences, Gainesville, FL. 30 pp.

Comment ID: 1476-2.001.044 Response: EPA disagrees that ANCOVA is a necessary analysis to demonstrate similar responses of lakes to nutrients. EPA’s final rule TSD shows the similarity in the response for clear, high and low alkalinity lakes to TN and TP, respectively.

Comment ID: 1476-2.001.049 Response: EPA notes that it is not finalizing a specific conductance as an indicator for alkalinity. EPA also notes that it has revised the alkalinity threshold from proposed rule, 50 mg/L CaCO3, to 20 mg/L CaCO3 for final rule. In response to the commenters question regarding how lakes less than 50 mg/L CaCO are being considered for criteria development, or in the case of what is being finalized, 20 mg/L CaCO3, EPA concluded that it is appropriate to consider them with the clear, high alkalinity lakes for purposes of deriving numeric TN and TP criteria. EPA concluded that the chl-a criteria should be different for clear, low alkalinity lakes, but the TN and TP criteria could be derived based on consideration of all the data from clear, low and high alkalinity lakes.

Comment ID: 1355-2.001.030 Response: EPA disagrees that the criteria derived at proposed rule are unnecessarily over-protective of highly colored lakes. EPA considers the criteria at proposal and at final rule for colored lakes to be protective of highly colored lakes, particularly in the event where highly colored lakes may exhibit less light limitation (i.e., less color) over time. EPA relied upon the nutrient vs. TN, TP relationships in intermediate colored lakes (color ranging between 40 and 140 PCU) to protect all lakes with color above 40 PCU. See the final rule TSD for more detail.

Comment ID: 1474-1.001.083 Response: EPA disagrees the commenter’s assertion that the variable TN, TP concentrations associated with a given chl-a concentration result in an unreliable indicator of water quality impairment. EPA takes the view that the range in TN and TP concentrations reflect the variability in lake nutrients over time. Based on that variability, EPA constructed a framework within which TN and TP can be modified provided that the chl-a criteria are met. EPA considers this approach to be flexible, scientifically-based as indicated by the regression analysis, and based on the observed variability that the commenter points out. See TSD for additional detail.

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Comment ID: 1836.001.016 Response: EPA thanks the commenters for supporting EPA’s chl-a criteria. To the comments that suggest the baseline and/or modified TN and TP criteria might be too restrictive, EPA recognizes that the broad approach taken in proposed rule and in final rule may not reflect certain lake-specific conditions. EPA’s basis for the baseline and modified criteria relies on the best available data. See TSD for additional detail.

Comment ID: 1355-2.001.020 Response: EPA recognizes the effect log scale has on interpreting the seasonal differences between chl-a in clear and colored lakes. EPA considers a log scale to be the most appropriate graphical approach to capturing and summarizing the range in chl-a. Water chemistry data, including chl-a, were natural log (ln) transformed prior to analysis to adhere to assumptions regarding normality required of many parametric statistical tests and to reduce the influence of extreme values typical of log-normally distributed nutrient concentration data on estimates of central tendency (e.g., Zar 1996). EPA’s analysis of lakes with paired summer and winter observations showed that there is a tendency for summer chl-a values to be higher. The mean seasonal difference was 6% in clear lakes, 26% in moderately colored lakes, and 77% in dark-colored lakes. An increase in productivity in summer is to be expected. The seasonal difference is statistically significant, but it is small and negligible in the context of overall variability among lakes, and for development of nutrient criteria for clear and moderately colored lakes. The nutrient criteria for dark-colored lakes are derived from the nutrient distributions, and not from the regressions, so seasonal differences in chlorophyll are not applicable. EPA does not think the differences in clear and moderately colored lakes are sufficient to derive seasonally adjusted criteria. Zar, J.H. 1996. Biostatistical Analysis. Third Edition. Prentice-Hall.

Comment ID: 1476-2.001.048 Response: EPA’s final rule does not establish or modify any designated uses. The criteria EPA is finalizing are intended to protect the Class I and Class III designated uses Florida already has in place. The federal numeric nutrient criteria would not apply where and when the use is something other than Class I or Class III. If a discharger requests a variance, Florida may use its own variance process to temporarily modify the use if appropriate and submit such variance to EPA for review under the CWA. 

# CHAP1C - 1C. METHODOLOGY FOR PROPOSED TP AND TN CRITERIA IN LAKES Comment ID 0974.001.011
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago

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4. Page 1-15 states, "Because algal response is influenced by factors other than nutrients (grazing, macrophyte, nutrient uptake, water retention time), the most scientifically defensible strategy for managing nutrients within the range of uncertainty is to verify a biological response before taking management action." The District disagrees with EPA's method of using "the lower and upper TN and TP values derived from the 50`h percentile prediction interval of theregression" (Federal Register Vol. 75, No. 16, p. 4187) for the range of modified criteria. Since the ambient-based, lakespecific, modified TP and TN criteria are allowed in the proposed rule (see footnote C of the table for Proposed Numerical Criteria for Lakes, Federal Register Vol. 75, No. 16, p. 4184), the District recommends using 90`h percentile prediction interval of the regression for setting the lower and upper values as the ranges of modified criteria. 

# Comment ID 1355-2.001.021
Author Name: Barker V. Organization: Brevard County Board of County Commissioners While not explicitly stated in the rule, the authors of the TSD (page 1-14) state that regression relationships tended to under-predict chlorophyll a in moderately colored lakes (40-140 PtCo units) and over-predict chlorophyll a in highly colored lakes(>150 PtCo units). The authors in the technical guidance document concluded on page 1-14 that "fully protective criteria for these systems can be developed on the basis of response relationships from moderately colored lakes (40- 140 PtCo units), although the criteria will likely be somewhat overprotective, given that high color will reduce algal response and biomass". 

# Comment ID 1355-2.001.027
Author Name: Barker V. Organization: Brevard County Board of County Commissioners The criteria development is derived based on a simple linear regression between nutrients and chlorophyll concentrations. The threshold chlorophyll values are used to estimate the nutrient concentration that would result in the threshold value. This "inverse prediction" was then used as the basis for the nutrient criterion. There are several inaccurate statements in the description of what a regression line and prediction interval is in the TSD and the rule. On page 1-14 it is stated that "the regression line and equation define the average relationship (i.e., half the points fall above the line and half below it). This statement is not accurate. While the regression line can be thought of as the mean response given a value of x, it is not true that it separates the data into two even groups. For example, consider a hypothetical relationship between x (Nitrogen) and y (chlorophyll a). For this example, 50 data points were generated from a normal distribution for both x and y and y was a function of x (i.e., y=5+2x+e). The term e refers to the error term in a regression equation and this term was generated based on a normal distribution with mean = 0 and standard deviation of 1. To facilitate the understanding of how particular data points can influence the regression estimate, y values corresponding to x values near the mean of x (i.e., between 0.4 and 0.6) were adjusted to be approximately twice the mean response of y (i.e., y+6). The results are plotted in Figure 3 below. One can see how these adjusted points have influenced the regression line upward and resulted in a regression line with 16 points above

11/19/2010 02:48 PM EST 2-4710Chapter 2 - Comment Documents Technical Support Document the line and 34 below the line. Therefore, EPA's assumption that a regression line will always split the data in half is incorrect. Further, it is implied on page 1-14 of the TSD that the bounds of the 50% prediction intervals represent the 25th and 75% percentile on the distribution. However, they seem to be referring to the independent variable rather than the response variable. That is, they consider "nutrient concentrations between a level that is unlikely (e.g. 25% probability) to elicit a given threshold of response and a level that is likely to elicit a response (e.g. 75% probability)". This is a gross misinterpretation of confidence intervals. EPA reports this range as "within the range of nutrient concentrations (between the upper and lower prediction interval).....". The prediction intervals are constructed to capture the uncertainty in the response variable at a given (fixed) level of x. EPA appears to be using inverse prediction logic to assume that the response level is fixed and that the nutrient level can be a range of nutrient concentrations between the left side and right side of the prediction interval for a fixed level of y. However, inverse prediction will not result in equivalent values when there is uncertainty in the relationship between x and y (see line of organic correlation; Helsel and Hirsh, 2002). EPA‘s application to derive numeric nutrient criteria seems to use a unique approach and it would benefit water resource managers to understand the scientific foundation for such an approach based on citing references to supporting literature or previous applications of this approach. Furthermore, since the regression equations were derived on log transformed data (e.g., Figure 1-11 in the TSD), the variance estimates are "squashed" and back calculation of the prediction estimates on the log scale will not provide accurate estimates of the true prediction intervals on the natural scale (see Helsel and Hirsh 2002; page 255). This "smearing" effect will corrupt the identification of EPA proposed numeric nutrient criteria based on their derivation using the log-log regressions and the 50% prediction interval. Original comment letter contains additional information in Figure 3. Regression line based on simulated data illustrating that a simple linear regression line will not always divide the data into two groups with equal sample size as postulated in EPA TSD. See original comment letter. 

# Comment ID 1476-2.001.050
Author Name: Wehle C. Organization: South Florida Water Management District Page 14 There are also strong relationships among TP, TN, and color. Thus, light is limited because of higher color, TN and TP, making chlorophyll values lower. 

# Comment ID 1476-2.001.051
Author Name: Wehle C. Organization: South Florida Water Management District Page 14

11/19/2010 02:48 PM EST 2-4711Chapter 2 - Comment Documents Technical Support Document "Regional differences among the moderately colored lakes (color between 40 and 140 PCU) were evaluated, but USEPA found that those colored lakes show similar chl. a responses regardless of location, although there were differences in the range of nutrient concentrations (Figures 1-9 and 1-10)." USEPA should demonstrate this statistically using analysis of covariance (it appears that the slopes and positions of the curve are quite different). 

# Comment ID 1476-2.001.052
Author Name: Wehle C. Organization: South Florida Water Management District Page 14 "Without a strong and robust nutrient-chl. a relationship in the highly colored (> 140 PCU) lakes, fully protective criteria for these systems can be developed on the basis of the response relationships from the moderately colored lakes (40­ 140 PCU), although the criteria will be somewhat overprotective, given that high color will reduce algal response and biomass." If TP and TN are not related to chlorophyll a in highly colored lakes, then using a surrogate to impose a standard is not logical because based on the chlorophyll a standard only five or six of these highly colored lake samples exceed the standard. Most meet the standard throughout the range of TN and TP values. Setting TN and TP values would misclassify most of these lakes as impaired when they are not. 

# Comment ID 1476-2.001.053
Author Name: Wehle C. Organization: South Florida Water Management District Page 14 Given this approach and using annual average chl. a values of 20 ug/L for colored lakes and higher-specific conductance clear lakes, and 6 ug/L for clear, low-specific conductance Florida lakes, respectively, criteria ranges associated with protection of designated uses can be defined on the basis of the 50% prediction intervals depicted in Figures 1-11 and 1-13." The axes should be reversed. Since you are trying to define TP and TN values based on chlorophyll a of 20, then the independent variable is chlorophyll a and TN and TP are the dependant variables



# Comment ID 1476-2.001.054
Author Name: Wehle C. Organization: South Florida Water Management District Page 14 "Results indicate that a 5-year rolling average was generally sufficient to ensure minimization of the variance (for an

11/19/2010 02:48 PM EST 2-4712Chapter 2 - Comment Documents Technical Support Document example data set, see Figure 1-14). Yet a 7-year average is the basis to determine color in the rule. 

# Comment ID 1836.001.017
Author Name: Moore D. Organization: Southwest Florida Water Management District 7. USEPA should conduct additional analyses to refine chlorophyll a targets for highly colored lakes. USEPA noted that the proposed colored lake chlorophyll a criterion for highly colored lakes (lakes with greater than 140 PCU) is "somewhat overprotective" because the relationships between nutrients and chlorophyll a are weak (page 1-14, Technical Support Document) . The extent to which color explains the variability of chlorophyll a in colored lakes needs to be determined . A more detailed multivariate regression analysis including color and nutrients as explanatory variables should be conducted to determine the strength of the relationship between these two variables . These analyses will help to reduce the level of uncertainty in the relationship between nutrients and chlorophyll a in highly colored lakes . 

# Response
Comment ID: 1476-2.001.054 Response: For final rule, EPA stipulates that the long-term color provided in the lake’s available data record should be used as one of the factors that would determine the applicable criteria for a given lake. The lake’s long-term alkalinity is also needed to determine the applicable lake criteria.

Comment ID: 1476-2.001.053 Response: EPA disagrees that the axes should be reversed in the linear regression between nutrients and chl-a. EPA considers chl-a (y-axis) to be the variable of interest that responds as a function of nutrients, TN and TP (x-axis). EPA has considered inverse regression (predicting nutrients from observed chlorophyll values), but inverse regression does not address the issues of nutrient criteria. The objective of criteria development is not to estimate the nutrient concentration that yields chlorophyll of 20 ug/L, but to derive nutrient concentrations where there are 25% and 75% risks of chlorophyll exceeding 20 ug/L. In other words, the predicted distribution of chlorophyll, given a particular nutrient concentration, is the quantity of interest, and to estimate this predicted distribution, a conventional linear regression, with nutrient concentrations as the explanatory variables and chl-a as the response variable, is most appropriate.

Comment IDs: 1836.001.017 , 1476-2.001.052, 0974.001.011, 1355-2.001.021 Response: EPA disagrees that a multivariate analysis is necessary to determine chl-a thresholds for highly colored lakes. EPA also disagrees that the criteria derived at proposed rule are unnecessarily over-protective of highly colored lakes. EPA considers the

11/19/2010 02:48 PM EST 2-4713Chapter 2 - Comment Documents Technical Support Document criteria at proposal and at final rule for colored lakes to be protective of highly colored lakes, particularly in the event where highly colored lakes may exhibit less light limitation (i.e., less color) over time. EPA relied upon the nutrient vs. TN, TP relationships in intermediate colored lakes (color ranging between 40 and 140 PCU) to protect all lakes with color above 40 PCU. See the final rule TSD for more detail.

Comment ID: 1476-2.001.051 Response: EPA disagrees that ANCOVA is a necessary analysis to demonstrate similar responses of lakes to nutrients. EPA’s final rule TSD shows the similarity in the response for clear, high and low alkalinity lakes to TN and TP, respectively.

Comment ID: 1476-2.001.050 Response: EPA agrees with commenter that higher color in lakes may result in light limitation of algal growth.

Comment ID: 1355-2.001.027 Response: EPA has considered the issues of back transformation cited from Helsel and Hirsch (2002). The problems with log transformations and back-transformations apply only to mass loading estimation, where total loading is indeed the sum ofuntransformed loading estimates. Since the lake criteria are expressed in concentrations, not loads, concerns about backtransformation of means are not relevant. EPA agrees that the statement "half the points fall above the line and half below it" is incorrect. The regression line is an estimate of the mean response, not of the median. Statements to this effect have been corrected in the final rule TSD. 

# CHAP1D - 1D. DURATION AND FREQUENCY FOR PROPOSED LAKES CRITERIA Comment ID 2018-6.001.008
Author Name: McLean J. Organization: City of Tampa 20. There are several inaccurate statements in the description of what a regression line and prediction interval is in the TSD and the rule. It is stated that "the regression line and equation define the average relationship (i.e., half the points fall above the line and half below it)." This statement is not accurate. While the regression line can be thought of as the mean response given a value of x, it is not true that it separates the data into two even groups. 

# Response

11/19/2010 02:48 PM EST 2-4714Chapter 2 - Comment Documents Technical Support Document

Comment ID: 2018-6.001.008 Response: EPA agrees with the comment that the regression line represents the mean response and not the median response. The regression discussion has been revised in the final rule TSD and statements to this effect have been corrected.



# CHAP1E - 1E. APPLICATION OF LAKE-SPECIFIC AMBIENT CALCULATION PROVISION FOR ALTERNATIVE TP AND TN CRITERIA Comment ID 0974.001.010
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago 3. Strong evidence, as shown in Figure 1-7 on pages 1-28 of TSD, indicates that chlorophyll a concentrations are inversely correlated to annual geometric mean lake color. The District suggests that EPA incorporate lake color into formulating the numerical nutrient criteria for the colored lakes in Florida, in addition to the consideration of regional differences. Applying the numeric nutrient criteria developed based on the moderately colored (>40 - 140 PCU) Florida lakes to the heavily colored (> 140 PCU) Florida lakes is overly protective and will result in spending unnecessary resources to restore the heavily colored (> 140 PCU) Florida lakes and streams feeding to these lakes to meet the proposed criteria with no tangible benefits . 

# Comment ID 1476-2.001.055
Author Name: Wehle C. Organization: South Florida Water Management District Page 17 "The 50% prediction interval is the range within which one-half of chl. a observations are expected to fall for a given nutrient concentration (TN or TP), centered on the mean expectation at the regression line. In other words, the lower and upper bounds approximate the 25th and 75th percentiles of expected chl. a response for the given TN or TP, as predicted by the regression equations (Figures 1-11, 1-13)." See comment 13 above. 

# Response
Comment ID: 1476-2.001.055

11/19/2010 02:48 PM EST 2-4715Chapter 2 - Comment Documents Technical Support Document

Response: EPA agrees with the comment that the regression line represents the mean response and not the median response. The regression discussion has been revised in the final rule TSD and statements to this effect have been corrected.

Comment ID: 0974.001.010 Response: EPA disagrees that the final criteria are unnecessarily over-protective of highly colored lakes. EPA considers the criteria for colored lakes to be protective of highly colored lakes, particularly in the event where highly colored lakes may exhibit less light limitation (i.e., less color) over time. EPA relied upon the nutrient vs. TN, TP relationships in intermediate colored lakes (color ranging between 40 and 140 PCU) to protect all lakes with color above 40 PCU. See the final rule TSD for more detail. 

# CHAP1F - 1F. ALTERNATIVES CONSIDERED BY U.S. EPA Comment ID 0974.001.012
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago 5. Figures 1-4 and 1-5 on pages 1-26 and 1-27 present the separate analysis on the relationship between chlorophyll a concentrations and TP or TN concentrations in Florida lakes. It has been reported (Correll, 1998. J. Environ. Qual. 27 :261-266) that excessive concentration of phosphorus is the most common cause of eutrophication in freshwater lakes, reservoirs, streams, and headwaters of estuarine systems and in the ocean, N becomes the key mineral nutrient controlling primary production . The District suggests that EPA conduct data analysis to investigate whether phosphorus concentrations at the levels of the proposed criteria become the limiting factor to lake eutrophication, and the numeric criteria for nitrogen be dropped if P is the limiting actor. 

# Comment ID 1476-2.001.056
Author Name: Wehle C. Organization: South Florida Water Management District Page 19 "...the cool season (October to April) and the warm season (May to September)." For the southern part of the state these are considered dry (October to April) and wet (May to September) seasons. 

# Comment ID 1476-2.001.057
Author Name: Wehle C. Organization: South Florida Water Management District

11/19/2010 02:48 PM EST 2-4716Chapter 2 - Comment Documents Technical Support Document Page 19 TP, TN, chlorophyll, and specific conductance are all correlated with alkalinity in the described data set (Figure 1-16)."The data are compressed by the natural log. USEPA should provide figures showing results if the data are untransformed. 

# Comment ID 1476-2.001.058
Author Name: Wehle C. Organization: South Florida Water Management District Page 19 "The acidic and alkaline lakes appeared to lie on the same regression relationship, although alkaline lakes had higher mean nutrient and chlorophyll concentrations." USEPA should use analysis of covariance to demonstrate this. 

# Comment ID 1836.001.014
Author Name: Moore D. Organization: Southwest Florida Water Management District 4. If USEPA chooses not to employ the alternative region-based classification scheme for distinguishing clear-alkaline from clear-acidic lakes, it should use the alternative total alkalinity classification breakpoint of 20 mg/L instead of the originally proposed 50 mg/L. This recommendation is based on USEPA's statement in the proposed rule's Technical Support Document that "if the class breakpoint is at 20 mg/L, as suggested by the change point analysis, the separation of the alkalinity classes is more distinct" (page 1-20, Technical Support Document). 

# Comment ID 1836.001.024
Author Name: Moore D. Organization: Southwest Florida Water Management District 14. USEPA's assumptions of a normal statistical distribution may have been violated in the analysis of total phosphorus, total nitrogen, and chlorophyll a; SWFWMD recommends using a non-parametric technique . The alternative "distributional" approach involves assumptions about the normality of TP, TN and chlorophyll a measurements that may not be valid (page 1-21, Technical Support Document) . Probabilities for individual observed values, such as annual geometric means or other statistics, could instead have been calculated using bootstrapping techniques to create distributions not confined by normality assumptions. 

# Response

11/19/2010 02:48 PM EST 2-4717Chapter 2 - Comment Documents Technical Support Document

Comment ID: 1476-2.001.058 Response: Regression analyses of clear, low alkalinity lakes are confounded by multiple detection limits in the data set, especially for TP and chl-a. The chl-a measurement used was corrected chl-a, and thus relies on measurement of uncorrected chl-a and on phaeophytin. While the published method detection limit is less than 1 ug/L, these data relied on measurements from multiple laboratories, increasing the likelihood of detection limit error in uncorrected chl-a, phaeophytin, or both. EPA removed reported TP less than 0.005 mg/L and chl-a less than 1 ug/L, but some detection limits were higher than these, there was clearly increased variability of TP and chl-a at low concentrations. ANCOVA of high and low alkalinity clear lakes showed significantly different slopes, but this was entirely due to outliers and potential detection limit errors at low concentrations. Visual inspection of the data revealed that clear, low alkalinity lakes appeared to lie on the clear, high alkalinity regression line, except for lakes with the lowest chl-a and TP concentrations. To reduce the effect of these errors, EPA combined low and high alkalinity lakes into a single regression. After development of a more precise data set with uniform and low MDL, FDEP may choose to revise the criteria for clear, low alkalinity lakes.

Comment ID: 1476-2.001.056 Response: EPA appreciates the comment clarifying the seasons. EPA has considered this comment in preparing the final rule and TSD.

Comment ID: 1476-2.001.057 Response: EPA recognizes the effect log scale has on interpreting the seasonal differences between chl-a in clear and colored lakes. However, EPA considers a log scale to be the most appropriate graphical approach to capturing and summarizing the range in water quality data such as TN, TP, chl-a, and alkalinity. Water chemistry data, including chl-a, were natural log (ln) transformed prior to analysis to adhere to assumptions regarding normality required of many parametric statistical tests and to reduce the influence of extreme values typical of log-normally distributed nutrient concentration data on estimates of central tendency (e.g., Zar 1996).
References: Zar, J.H. 1996. Biostatistical Analysis. Third Edition. Prentice-Hall.

Comment ID: 1836.001.024 Response: EPA tested the normality of the log-transformed variables TP, TN, and chl-a. Normal probability plots showed a straight line with deviations from normality at the lower and upper ends (See the final rule TSD). Deviations at small values are most likely due to detection limits, and the deviations at high values may be due to truncation of extreme values unlikely to occur in real lakes. Statistical tests of normality of the transformed data (chi-square, K-S, Shapiro-Wilk) all revealed statistically significant non- normality due to the ends of the distributions. This is a typical example where a large sample size results in statistical significance, but the effect of the non-normal distribution is of no practical significance; it is negligible because the sample size (N) was large(

11/19/2010 02:48 PM EST 2-4718Chapter 2 - Comment Documents Technical Support Document N=1340 for annual means; N > 5000 for individual observations), and also because outliers affected the tests. In particular, there were clusters of detection limit observations for TP and chlorophyll at the low end of the detection range. At the highest chlorophyll concentrations, extreme values were less frequent than expected, possibly due to physical constraints (e.g., light limitation) on chl-a concentration (See the final rule TSD). Regression is robust to minor deviations from normality (e.g., Zar 1996).
References: Zar, J.H. 1996. Biostatistical Analysis. Third Edition. Prentice-Hall.

Comment ID: 0974.001.012 Response: EPA disagrees with the comment suggesting that EPA determine the limiting nutrient for a given lake, then derive numeric nutrient criteria for the causal variable, TN or TP, that is limiting. EPA’s policy, and supporting scientific rationale, for deriving numeric nutrient criteria for both causal variables, TN and TP, is well-established (U.S. EPA 2000, Grubbs 2001, Grumbles 2007). EPA’s position has been further supported by independent, nationally recognized scientists who have concluded that prevention of eutrophication can best be achieved by controlling both nitrogen and phosphorus (U.S. EPA SAB 2007, Paerl, H.W. 2009, Conley et al. 2009). EPA refers the commenter to these documents for more detail on EPA’s scientifically-based position regarding dual nitrogen and phosphorus criteria.
References:
U.S. EPA. 2000. Nutrient Criteria Technical Guidance Manual: Lakes and Reservoirs. Office of Water, Washington, DC. EPA822-B-00-001. Grubbs, G. 2001. U.S. EPA. Memorandum to Directors of State Water Programs, Directors of Great Water Body Programs, Directors of Authorized Tribal Water Quality Standards Programs and State and Interstate Water Pollution Control Administrators on Development and Adoption of Nutrient Criteria into Water Quality Standards. November 14, 2001. Grumbles, B.H. 2007. U.S. EPA. (Memorandum to Directors of State Water Programs, Directors of Great Water Body Programs, Directors of Authorized Tribal Water Quality Standards Programs and State and Interstate Water Pollution Control Administrators on Nutrient Pollution and Numeric Water Quality Standards. May 25, 2007.
U.S. EPA. 2007. Hypoxia in the Northern Gulf of Mexico: An Update by the EPA Science Advisory Board. EPA Science Advisory Board, Washington, D.C. EPA-SAB-08-003 Paerl, H.W. 2009. Controlling Eutrophication along the Freshwater–Marine Continuum: Dual Nutrient (N and P) Reductions are Essential. Estuaries and Coasts. 32:593-601. Conley, D.J., H. W. Paerl, R.W. Howarth, D. F. Boesch, S.P. Seitzinger, K.E. Havens, C. Lancelot, G.E. Likens. 2009. Controlling Eutrophication: Nitrogen and Phosphorus. Science. 323:1014-1015.

11/19/2010 02:48 PM EST 2-4719Chapter 2 - Comment Documents Technical Support Document

Comment ID: 1836.001.014 Response: EPA agrees with the commenter. Based on EPA’s analysis of alkalinity data (see final rule TSD), EPA is finalizing Florida’s lake classification based on an alkalinity and color threshold as follows: Clear lakes (color <= 40 PCU) with low alkalinity (< =20 mg/L CaCO3) Clear lakes (color <= 40 PCU) with high alkalinity (>20 mg/L CaCO3) Colored lakes (color >40 PCU) 

# CHAP2 - CHAPTER 2: STREAMS Comment ID 0896-1.001.007
Author Name: * * Organization: Lee County Division of Natural Resources Chapter 2, Figure 2-5 Page: 2-60 Could we get the GIS coverages for the NWR eco-regions to help verify the local perspective? 

# Comment ID 0896-1.001.008
Author Name: * * Organization: Lee County Division of Natural Resources Chapter 2, Figure 2-23 Page: 2-73 It is not clear looking at this graphic what constitutes an estuary as opposed to a watershed in many cases. Is the thin dark blue margin along the coastline estuary? In the case of the Caloosahatchee, the main stem of the river is the estuary due to the S-79 lock structure. This is a concern for us given that we have NPDES outfalls in the Tidal Caloosahatchee and need to know what criteria apply to our point source outfalls, if a mixing zone will be allowed for our NPDES outfalls and whether or not the tributaries below the S-79 lock structure are considered estuarine. Could we get the GIS coverage with attributes for this figure as well? 

# Response

11/19/2010 02:48 PM EST 2-4720Chapter 2 - Comment Documents Technical Support Document
Comment IDs: 0896-1.001.007, 0896-1.001.008 Response: In response to commenter’s requesting the GIS coverages for EPA’s Nutrient Watershed Regions, EPA provided GIS coverages as part of the Agency’s Supplemental Notice of Data Availability published in August 2010. EPA is also making available the coverages associated with the Nutrient Watershed Regions as described in final rule and the final rule TSD. With respect to the comment regarding the delineation separating estuaries from inland waters, EPA has operationally defined fresh waters in its final rule: “Consistent with rule 62-302.200, F.A.C., EPA’s final rule defines “predominantly fresh waters” to mean surface waters in which the chloride concentration at the surface is less than 1,500 milligrams per liter (mg/L).” 

# CHAP2A - 2A. METHODOLOGY FOR STREAM CLASSIFICATION: U.S. EPA’S NUTRIENT WATERSHED REGIONS (NWRS) Comment ID 0896-1.001.012
Author Name: * * Organization: Lee County Division of Natural Resources In general, Lee County is concerned that there are inconsistencies in methods used to develop stream and lake nutrient water regions. There appears to be alternation between geologic data and water column data when proposing NWRs for streams versus lakes. In addition, the terminology and physical descriptions used when discussing the NWRs are inconsistent in the TSD. The characterization of NWRs whether based on water quality or biology needs to be clarified. The biological evaluation tools used to define NWRs is not complete. There have been no stream condition or lake vegetation indices developed for South Florida and wetland health indices have not been developed nor are they being considered. While South Florida has a number of canals that must be accounted for there are many natural stream, wetland, coastal marsh and tidal mangrove areas that have not been considered and will have no paired biological data for developing numeric nutrient criteria. The work completed in South Florida to date relies heavily on data collected in canals and does not consider natural systems. Overall it appears that water quality criteria that are being developed for the South NWR is relying completely on canal data. In fact, there are numerous stream systems in the South NWR that are naturally occurring and that do not function like canals. 

# Comment ID 0896-1.001.014
Author Name: * * Organization: Lee County Division of Natural Resources The Caloosahatchee River has not been placed in an appropriate NWR because there are no valid biological evaluation tools available for the watershed. Lee County believes that the Caloosahatchee basin should be part of the South Florida NWR and not the Peninsular NWR.

11/19/2010 02:48 PM EST 2-4721Chapter 2 - Comment Documents Technical Support Document


# Comment ID 0974.001.019
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago 2. A nutrient watershed regions approach was taken for developing numeric nutrient criteria for the streams in Florida (described in TSD section 2a). 

# Comment ID 0974.001.021
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago The following are the comments on Chapter 2: Methodology for Deriving EPA's Proposed Criteria for Streams of TSD for EPA's Proposed Numeric Nutrient Criteria for Florida Inland Surface Fresh Waters. 1 . The District welcomes EPA's nutrient watershed regions approach (section 2a of TSD on pages 2-1 through 2-3) for developing numeric nutrient criteria for the streams in Florida. 

# Comment ID 1368-1.001.029
Author Name: Waters D. Organization: City of Miami Department of Public Works Subdivide South Florida after DEP's Level IV Subecoregions for Florida Small / Wadeable Streams by Griffith 1994 as shown on page 59 in Proposed Methods and Approaches for Developing Numeric Nutrient Criteria for Florida's Inland Waters which is available online at http://www.regulations.gov/search/Regs/home.html#docketDetail?R=EPA-HQ-OW
2009-0596. 

# Response
Comment ID: 0896-1.001.012 Response: In response to concerns regarding classification of streams and lakes and the basis for using biological tools in classification, EPA points out that the SCI was not used in classifying streams and rivers, only in deriving criteria. EPA recognizes the issue raised by the commenter regarding the use of biology in deriving regions. However, while FDEP’s bioregions played a role in exploring classifications, as detailed in the proposed rule TSD, the regionalizations are largely based on natural differences in underlying geology and the bases for expectations of nutrient dynamics and nutrient responses across the State. In a similar

11/19/2010 02:48 PM EST 2-4722Chapter 2 - Comment Documents Technical Support Document manner, lake classifications were based on differences in underlying functional responses of chl-a to nutrients across lake types. The commenter is also referred to the final rule TSD for detailed explanations of lake and stream classifications beyond that already detailed in the proposed rule TSD. Some alterations instream classifications were made, largely to reflect, again, natural geologic differences with relation to nutrient dynamics. At proposal EPA employed an alternative reference condition-based approach to derive stream criteria. This approach relied on the use of sites known to be biologically healthy based on an SCI score. This approach does not preclude the use of distributions defined using other selection or screening criteria to identify a reference population. In fact EPA included at proposal, and is finalizing in final rule, a modified Benchmark Distribution Approach, which relied on selection criteria other than SCI scores to identify a reference population. It is not necessary, therefore, to have a biological tool to define a population of sites from which to derive a criterion using the reference condition based approach and this is consistent with EPA guidance on reference condition based approaches.
Comment ID: 0896-1.001.014 Response: EPA included the Caloosahatchee River in the Peninsula Region in its stream regionalization because EPA found no evidence to suggest that biological responses in this river should be demonstrably different from those in river/stream systems of the Peninsula Region. As for other flowing waterbody types mentioned (i.e., canals in South Florida), those waters are outside the scope of EPA’s final rule and will be addressed in EPA’s proposed rule for Florida’s estuarine and coastal waters in 2011.
Comment ID: 1368-1.001.029 Response: EPA thanks the commenters for providing information regarding classification of South Florida after FDEP’s Level IV Subecoregions. However, EPA has decided to defer final rulemaking for inland flowing waters in South Florida. EPA will address the issue of classification of inland flowing waters in South Florida in its proposed rule for Florida’s estuarine and coastal waters in 2011. EPA encourages the commenter to review the Agency’s 2011 proposed rule and submit public comments at that time. Comment IDs: 0974.001.019, 0974.001.021 Response: Do not require response.



# CHAP2B - 2B. THE USE OF THE STREAM CONDITION INDEX AS AN INDICATOR FOR ESTABLISHING BIOLOGICALLY HEALTHY CONDITIONS Comment ID 0896-1.001.013
Author Name: * *

11/19/2010 02:48 PM EST 2-4723Chapter 2 - Comment Documents Technical Support Document Organization: Lee County Division of Natural Resources To date DEP has not developed stream condition indexes that are applicable south of the Caloosahatchee Basin. Biological criteria for the South NWR should be developed for natural stream systems prior to adopting a blanket criteria based on canals. 

# Comment ID 0974.001.014
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago The range may be derived using 50th percentile and the highest concentrations as the lower and upper bounds from a data set for all streams that are deemed biologically healthy through the analysis as described in section 2b of TSD on pages 2-3 through 2-8. A stream condition index (SCI) score of 34 should be used as this corresponded to expert consensus for a biologically healthy stream in Florida (as stated on pages 2-7). 

# Comment ID 1011.001.008
Author Name: Todd, Jr. K. Organization: Palm Beach County 5) In its technical support document, "Florida Nutrient Benchmark Distributional Approach for Rivers and Streams", DEP has concluded that the use of the 90th percentile of nutrient concentration derived from distribution of minimally disturbed streams is inherently protective of aquatic life. The documentation of these healthy biological communities demonstrates that aquatic uses are fully met within the associated range of nutrients. It is the County's belief that use of a 75th percentile would result in an excessive error, with a large number of healthy sites incorrectly classified as impaired. In fact, in a presentation made to the Florida House Agriculture & Natural Resource Policy Committee earlier this month, the DEP stated that over 80% of the State's pristine water bodies would be considered impaired by the proposed standards. It would appear that EPA is taking an extremely restrictive approach, establishing criteria which would unnecessarily require that resources be expended to address waters that do not need them. Considering all factors, we all need to work collaboratively to establish standards that do not achieve this kind of a result. 

# Comment ID 1292-1.001.088
Author Name: Wiegand P. Organization: National Council for Air and Stream Improvement, Inc. Unfortunately, the criteria proposed by EPA for flowing waters of different nutrient watershed regions are not accompanied by detailed, well-described conceptual models. While supporting text in Chapter 2 of the EPA TechnicalSupport Document "Methodology for Deriving U.S. EPA's Proposed Criteria for Streams" (docket file EPA-HQ-OW11/19/2010 02:48 PM EST 2-4724Chapter 2 - Comment Documents Technical Support Document 2009-0596-0003.2.pdf) describes some of the basis for the regionalization scheme established for streams, this description emphasizes conditions present within the regions (e.g., geology, nutrient regimes, biological communities). Not included in the discussion is a description of how the ecosystems in each region differ with respect to conditions of light, flow, temperature, water chemistry, and other factors that can influence biological responses to changing nutrient conditions; that is, how each group of flowing water ecosystems is expected to respond to nutrients. As a result, technical support documentation lacks a coherent, concise conceptual model of nutrient impacts at the level needed to support conclusions from the analysis of stressor-response data. Without detailed conceptual models, inconsistencies in the approaches used to derive criteria may be more likely. For example, it is unclear why the effects of water color on nutrient response are directly incorporated into the TN and TP nutrient criteria for lakes but not for flowing waters. This leaves the impression that the conceptual models for these waterbody types are poorly developed. Furthermore, the biological/ecological relevance of the criteria and of statistical associations and changepoints is much more difficult to judge without detailed conceptual models. EPA's draft empirical approaches guidance states that methods such as non-parametric changepoint analysis can reflect regions of more rapid response to changing nutrient concentrations, and therefore may be used as bases for deriving numeric nutrient criteria. However, as described above, apparent changepoints in responses, including those found to be statistically significant, may or may not provide a useful basis for criteria derivation. This topic must be addressed carefully during criteria development to minimize the opportunity for making inappropriate assumptions about the nature of the stressor-response relationship. The SAB Committee draft report states: "In Subsection 4.3 of the Guidance, more detail should be provided in the discussion of conditions under which the last two methods, non-parametric changepoint analysis (nCPA) and discontinuous regression, should be applied (other than simply stating that they should be used when a direct designated use impairment threshold is unavailable). In addition, the Committee notes that a curved response: 1) may or may not be real; 2) may or may not signal an impaired designated use; and 3) may or may not be indicated at all by the data." (SAB Committee report, page 34-35). Need to Emphasize Primary Response Variables in Justification of Nutrient Criteria One important and essentially uncontroversial element of even a general conceptual model of nutrient impacts (such as presented in Fig. 10 of the draft empirical approaches guidance) is the position of aquatic plants as a primary response variable. Interactions among nutrient concentrations, light, temperature, flow, and other factors are expected to result first in changes to plant/algal growth and/or microbial growth. Such changes may in turn modify environmental conditions such as DO, pH, habitat, food, and perhaps other factors in ways that affect secondary impacts; that is, changes in macroinvertebrate and fish communities. Interpreting associations from field data between nutrients and secondary response variables (whether weak or strong) as 67 cause-effect relationships when few data are available or no relationships are observed between nutrients and primary response variables leaves a major component of the conceptual model unconfirmed. Lacking confirmation, there is little or no basis for a cause-effect relationship and criteria derived using the presumption of cause-effect, including reference waterbody-based criteria, are essentially baseless. The Florida SCI provides a useful example to consider. It is used by FDEP as a metric of the health of the aquatic macroinvertebrate community in flowing waters, and therefore is one indicator of aquatic life designated use attainment.

11/19/2010 02:48 PM EST 2-4725Chapter 2 - Comment Documents Technical Support Document However, values indicating degraded conditions can result from a variety of stressors, possibly including but not limited to excessive nutrients. Environmental factors such as excess sedimentation, temperature, organic loading, and others also can negatively impact the SCI. Excess sediment may be accompanied by increased nutrient concentrations, and therefore statistical associations may occur between SCI and sediment as well as between SCI and nutrient concentrations. As Fig. 10 of the empirical approaches document indicates, excessive nutrients are expected to cause changes in SCI corresponding with excessive algae growth. Therefore, data from the aquatic plant community provide a critical component of the weight of evidence needed to support conclusions that statistical relationships, including observed changepoints, between nutrient concentrations and SCI reflect cause-effect. Where excess sedimentation is the primary cause of degraded macroinvertebrate communities, focusing management alternatives on nutrient reduction will not address the cause of the impaired condition, and SCI values would not be expected to improve. 

# Response
Comment ID: 0896-1.001.013 Response: One comment pointed out correctly that FDEP does not have an SCI for canals in South Florida. EPA has decided to defer final rulemaking for inland flowing waters in South Florida. EPA will address the issue of classification of inland flowing waters in South Florida in its proposed rule for Florida’s estuarine and coastal waters in 2011. EPA encourages the commenter to review the Agency’s 2011 proposed rule and submit public comments at that time.

Comment ID: 0974.001.014 Response: A second comment suggested that EPA use the SCI value of 34 rather than 40. EPA detailed its justification of an SCI threshold of 40 in the final rule TSD. EPA considered other values, including 34, but that value was considered inappropriate based on the analysis of the Biological Condition Gradient data, specifically the variability in expert responses. The proportional odds model detailed and discussed in the final rule TSD details this issue. EPA concluded that this analysis supported the SCI 40 threshold. Also, EPA considered a range approach for streams but could not develop a similar scientifically defensible approach for streams.

Comment ID: 1011.001.008 Response: EPA considered a variety of percentiles based on its understanding of the condition of waterbodies comprising the reference populations (benchmark and SCI). Question the percentile EPA proposed (75th percentile) and asserted that many of Florida’s “pristine” streams would exceed EPA’s proposed criteria. EPA disagrees with the commenter’s assertion that the benchmark population reflects pristine or natural stream conditions. EPA’s investigation of the benchmark population indicated that there is some degree of human disturbance and potential disturbance. For example, many of the benchmark sites occurred on the Clean Water Act section 303(d) list for nutrients and/or dissolved oxygen (or other pollutants). Satellite photos also indicated substantial landscape disturbance in several of the benchmark watersheds. While EPA recognized these human influences, real or potential, the Agency concluded the benchmark population to be an appropriate reference population from which numeric nutrient criteria could be derived. Furthermore, EPA judged that after additional screening of benchmark sites, such as removing sites with

11/19/2010 02:48 PM EST 2-4726Chapter 2 - Comment Documents Technical Support Document nutrient or dissolved oxygen impairments, the 90th percentile is an appropriate choice for defining TN and TP criteria in streams. The one exception is the West Central Nutrient Watershed Region, where insufficient data led EPA to conclude that the 75th percentile of the SCI Population is an appropriate choice for defining TN and TP criteria in streams.
Comment ID: 1292-1.001.088

Response: The last comment related to conceptual models and consideration of other factors influencing stressor-response relationships in streams. EPA noted that conceptual models of nutrient effects do occur in the scientific literature. While EPA considered these models, for example stressor-response models, EPA decided the distribution-based approach was the most scientifically defensible approach for streams. Therefore, EPA found that inclusion of alternate factors in stressor-response modeling decisions is unnecessary. The comment suggests that site-specific criteria that incorporate these alternate factors would be more appropriate. With regards to site-specific characteristics, EPA agrees that many factors affect the influence of nutrients (and many other pollutants for that matter) on streams, including some of the ones suggested by the commenter. EPA does not preclude the development of site-specific nutrient criteria and has included a process for establishing such criteria in the rule. The commenter also suggested the use of field-derived relationships to support cause and effect models. Field-derived stressor-response analysis is only one mechanism to support a cause and effect relationship. Others include experimental evidence (both field and laboratory) as well as other scientific studies. If the commenter is suggesting that there is no basis for supposing an effect of nutrients on streams, EPA would refer the commenter to scientific evidence to the contrary (e.g., Carpenter et al. 1998, Wetzel 2001, Dodds 2002, Allan and Castillo 2007).
References: Allan, J. D. and M.M. Castillo. 2007. Stream Ecology: Structure and Function of Running Waters. 2nd Edition Springer. Carpenter, S.R., N.F. Caraco, D.L. Correll, R.W. Howarth, A.N. Sharpley and V.H. Smith. 1998. Nonpoint pollution of surface waters with phosphorus and nitrogen. Ecological Applications 8: 559-568. Dodds, W. K. 2002. Freshwater Ecology: Concepts and Environmental Applications. Academic Press. Wetzel, R.G. 2001. Limnology: Lake and River Ecosystems. Third Edition. Academic Press.



# CHAP2C - 2C. METHODOLOGY FOR CALCULATING IN-STREAM PROTECTION VALUES: THE NUTRIENT WATERSHED REGION DISTRIBUTION APPROACH

11/19/2010 02:48 PM EST 2-4727Chapter 2 - Comment Documents Technical Support Document 

# Comment ID 0974.001.015
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago 3. Page 2-10 states, "The in-stream protect nutrient criteria were based on this SCI threshold of 40. Analysis was also run based on SCI thresholds of 44, 50, and 65 . These results are included here as well." The locations for the results based on SCI thresholds of 44, 50, and 65 are not explicitly given in this section of TSD. Analysis should also be run based on SCI threshold of 34 and the results presented in the future technical support document. 

# Comment ID 0974.001.016
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago 4. Section 2c (vii) of TSD on pages 2-10 and 2-11 indicates that (1) the site average, (2) grab sample, and (3) site-year average data nutrient concentrations based on SCI thresholds of 40 were used in separate analysis to derive the 75th percentile values . The document also states on page 2-11, "The site average data based on SCI thresholds of 40 were used to derive the in-stream protective nutrient criteria." However, the document does not state where the results from other two sets of data are displaced, or whether the 75th percentiles values from the three set of data were compared. 

# Comment ID 0974.001.017
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago 5. Pages 2-12 state, "The 75th percentiles were selected as the upper bound of the greatest confidence in where biologically healthy conditions exist (figures 2-14 and 2-16). Beyond the 75th percentile, there is a marked decrease in the slope at the cumulative and empirical frequency distributions." This is inaccurate. Theoretically, the slope of cumulative frequency distribution curve of a normal distribution starts to decrease after its 50th percentile . The cumulative distribution curves in Figures 2-14 and 2-16 on pages 2-66 and 2-68 do not show "marked decrease" beyond 75th percentile, which correspond to 0.75 on the right vertical axis in the figures. This phenomenon is likely caused by the wide spread of nutrient concentrations (2 to 4 order of magnitude in natural-log scale) and supported by relatively large standard deviation of the data sets (compared to the corresponding mean values) reported in Table 2-4 on pages 2-40. 

# Comment ID 0974.001.022
Author Name: Kollias L.

11/19/2010 02:48 PM EST 2-4728Chapter 2 - Comment Documents Technical Support Document Organization: Metropolitan Water Reclamation District of Greater Chicago 2. The District disagrees with the EPA's distribution-based approach for developing numeric nutrient criteria for the Florida streams, as stated in section 2c of TSD on pages 2-8, because this approach does not address cause-response relationship between nutrient concentrations and stream impairments due to nutrients . As shown in Figure 2-8 on pages 2-62, many factors in addition to nutrients can influence the health of biota in a stream . To single out nutrients from so many factors is not a scientific approach. The District suggests that similar to the proposed numeric nutrient criteria for lakes, EPA propose baseline criteria using the 90th percentile of a data set for the biologically healthy reference streams (as described in section 2c [vii] and [viii] of TSD on pages 2-10 through 2-11) and modified criteria using a range with the requirements for deriving specific IPVs through comprehensive data analysis including all potential factors. 

# Comment ID 1761-3.001.031
Author Name: Merrill M. Organization: Hillsborough County 12. In general, the importance of hydrology, shading, local system alteration, and sediment oxygen demand (SOD) seems to be consistently under-emphasized in the Technical Supporting Documentation (TSD). These are generally highly site specific compounding factors, and the degree of expression of nutrients at any location is highly dependant upon them. This is further reason why the reference approach does not work well on a regional basis and creates significant additional site specific issues that would have to be dealt with using the SSAC process. 

# Comment ID 1805-3.001.032
Author Name: Gallagher J. Organization: Pasco County 12. In general, the importance of hydrology, shading, local system alteration, and sediment oxygen demand (SOD) seems to be consistently under-emphasized in the Technical Supporting Documentation (TSD). These are generally highly site specific compounding factors, and the degree of expression of nutrients at any location is highly dependant upon them. This is further reason why the reference approach does not work well on a regional basis and creates significant additional site specific issues that would have to be dealt with using the SSAC process. 

# Response Comment IDs: 0974.001.022, 1761-3.001.031, 1805-3.001.032 Response: EPA agrees with comments that suggest that site-specific characteristics and factors affect the influence of nutrient pollutants on streams. However, EPA disagrees with comments that assert that EPA did not consider site-specific information in

11/19/2010 02:48 PM EST 2-4729Chapter 2 - Comment Documents Technical Support Document deriving numeric nutrient criteria for Florida’s streams. EPA’s approach to numeric nutrient criteria development for Florida streams was based on a combination of broad geographical and hydrological factors as well as site-specific features of individual stream sites. EPA’s approach is described in the final rule and TSD. EPA explicitly considered and factored into its decision making process for identifying reference streams the specific land use characteristics of a stream site (i.e., LDI), the water quality conditions at a stream site (i.e., nitrate, nutrient or dissolved oxygen impairments), and the biological conditions as expressed through a macroinvertebrate survey score (i.e., SCI).
Comment ID: 0974.001.022 Response: EPA also disagrees with comments that suggest EPA control or manage factors other than nutrients, which can affect stream biota. EPA has identified nutrients as a pollutant that can be subject to regulation under section 303 of the Clean Water Act because nutrient pollution can directly impair designated uses or contribute as one of many stressors to the impairment of designated uses. As such, EPA is justified in promulgating numeric nutrient criteria in its final rule.
Comment ID: 0974.001.022 Response: EPA also disagrees with the comments that suggest EPA should take a similar stressor-response approach to criteria development for streams as it did for lakes, and not pursue a reference condition-based approach. In fact, EPA first consideredstressor-response approaches (see final rule TSD). While EPA’s analyses indicated there were statistically significant stressorresponse relationships in Florida streams, EPA concluded that it could not precisely identify thresholds where a numeric TN, TP, or other causal and response variable would be supportive of Florida’s designated uses. EPA points out that these analyses corroborate the long-standing stressor-response relationships found elsewhere in the scientific literature. EPA has provided examples of these relationships in its final rule and TSD. EPA concluded that a reference condition-based approach, which is consistent with EPA’s recommendations in its peer-reviewed technical guidance manuals for streams (U.S. EPA 2000), was an appropriate approach for deriving numeric nutrient criteria for Florida’s streams. Comment IDs: 0974.001.015, 0974.001.016 Response: EPA points out to commenters regarding concerns over SCI thresholds and data averaging methods that EPA evaluated thresholds and alternative averaging methods in a systematic, quantitative way. EPA refers commenters to the final rule TSD.
Comment ID: 0974.001.017 Response: It is unclear to EPA what question is posed in comment. However, the commenter’s observation regarding scale and variability support the percentile approach justified and used by EPA at proposal, as well as the shape of the CDF curves. In addition, while the commenter notes that slopes do indeed begin to decline at 50% along CDF curves, this is not the point of greatest decline - that begins after approximately 0.75, where the rate of slope decline increases rapidly to nearly zero at 100%.

11/19/2010 02:48 PM EST 2-4730Chapter 2 - Comment Documents Technical Support Document 

# CHAP2D - 2D. DURATION AND FREQUENCY FOR PROPOSED STREAMS CRITERIA No Comments are Applicable to this Issue Category, and Thus No Response is Necessary.


# CHAP2E - 2E. PROTECTION OF DOWNSTREAM ESTUARIES AND LAKES Comment ID 0896-1.001.001
Author Name: * * Organization: Lee County Division of Natural Resources During the review process we found EPA's definition of an estuary vague when applying it to the State's TMDL evaluation process and our monitoring program. The language used to characterize how and where the proposed criteria is applied is ambiguous and we recommend that EPA pay particular attention to clarifying language in the technical support documentation prior to finalizing the rule. 

# Comment ID 0974.001.009
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago These criteria will have significant impact on deriving downstream protection values (DPVs) for the streams flowing into lakes, as described in TSD section 2e (i). 

# Comment ID 0974.001.013
Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago For proper alignment with downstream protection (as described in section 2e of TSD on pages 2-13 through 2-30), the District suggests that separate instream protection values (IPVs) as numeric nutrient criteria be derived for each watershed with the end point being a lake or estuary. 

# Comment ID 0974.001.018

11/19/2010 02:48 PM EST 2-4731Chapter 2 - Comment Documents Technical Support Document

Author Name: Kollias L. Organization: Metropolitan Water Reclamation District of Greater Chicago 6 . Pages 2-27 states, "Analysis of ecological conditions in Florida estuaries and the relation to nutrient loading is ongoing and will be evaluated in greater detail over the next year." This indicates that EPA is not ready to propose DPVs for protecting downstream estuaries in Florida based on scientifically defensible approaches at this time. The District disagrees with EPA's approach of estimating protective TN loads for estuaries in Florida based on current TN loads and background TN loads derived from the SAGT regional SPARROW model, as described in section 2e (ii) on pages 2-17 through 2-20. There are major pieces of uncertainty in the regional SPARROW model, such as large annual variation in current TN loads to estuaries in Florida (pages 2-17) and large difference of wet atmospheric nitrogen deposition between NADP and SPARROW, ie. 300 kg/km2/y by NADP versus 125 to 175 kg/km2/y by SPARROW, pages 2-24 and 2-25. The District suggests that EPA_ drop Section III.C(6) (b) in the proposed rule (Federal Register Vol . 75, No. 16, p. 4199 through 4208) and wait until the analysis of ecological conditions in Florida estuaries and the relations to nutrient loading is complete. 

# Comment ID 1355-2.001.017
Author Name: Barker V. Organization: Brevard County Board of County Commissioners

- The residence time was arbitrarily set to 2.5 months which is a gross simplification that may not pertain to any individual lake in Florida, yet be accurate as an average of all lakes. This becomes problematic when it comes time for each individual stream which contributes flow to a lake to be evaluated.

- The assumption that 50% of the streamflow from a stream is delivered to the lake is likewise an arbitrary and gross estimation that is likely not relevant to any particular lake. The EPA recognized " only 20% of over 7,000 Florida lakes have streams flowing into them at all." How can EPA identify those lakes that receive at least 50% of the its total inflow from streams and on what basis do they make that assumption?

- It appears that the EPA calculation that reports the DPV as 0.12 mg/L did not take the square root of the lakes hydrologic retention time. This calculation error results in a more stringent criteria than if the calculation were to have been carried out appropriately. 

# Response Comment IDs: 0896-1.001.001, 0974.001.018 Response: EPA appreciates the comments submitted regarding downstream protection of estuaries (0896-1.001.001, 0974.001.018). EPA has deferred final rulemaking on downstream protection of estuaries to the Agency’s 2011 rulemaking on numeric nutrient criteria for Florida’s estuaries. This decision is consistent with what EPA indicated in its proposed rule signed by the EPA Administrator on January 15, 2010: “At this time, EPA plans to take final action with respect to downstream protection values for nitrogen as part of the second phase of this rulemaking process in coordination with the proposal and finalization of numeric

11/19/2010 02:48 PM EST 2-4732Chapter 2 - Comment Documents Technical Support Document standards for estuarine and coastal waters in 2011” (p. 4208, EPA-HQ-OW-2009-0596, FRL-9105-1). This decision facilitates coordination with the development of proposed estuarine and coastal water quality criteria. EPA will consider these comments as it develops the proposed rule on numeric nutrient criteria for Florida’s estuaries and coastal waters due to be published in November 2011. EPA encourages comments to consider providing comments on the 2011 proposed rule as part of that rulemaking process, which may reflect modifications to the downstream protection of estuaries approach described in the January 2010 proposed rule for Florida’s inland waters. Comment IDs: 0974.001.009, 0974.001.013, 1355-2.001.017 Response: EPA agrees with the comment that the IPVs calculated for streams will affect DPVs for lakes (0974.001.009). EPA’s intent at proposal and in its final rule is to assure that upstream nutrient criteria ensure the protection of downstream lakes. EPA considered the commenter’s suggestion of deriving criteria for a specific watershed draining to a lake or estuary (0974.001.013) and considered the comments critical of EPA’s assumptions regarding the Vollenweider model (1355-2.001.017). For final rule, EPA has provided a mechanism, through the modeling approaches described in final rule and TSD, to derive downstream protection values (DPVs) that reflect the site-specific characteristics of a given lake, which would in turn be applicable to the point at which an inflowing stream enters a particular lake. In cases in which data are not available for the provided modeling approaches, EPA has provided alternative approaches for specifying the DPV (see preamble). The Vollenweider model and the associated assumptions, as described at proposal, are not part of EPA’s final rule.



# CHAP2F - 2F. ALTERNATIVE APPROACH CONSIDERED BY U.S. EPA Comment ID 0896-1.001.006
Author Name: * * Organization: Lee County Division of Natural Resources Chapter 2f-xii Page: 2-38 There appears to be inconsistency in the use of names describing Nutrient Watershed Regions (NWR) and those used to describe Stream Bioregions. For instance, Stream Bioregion names such as Northeast Region are used inappropriately as a Nutrient Watershed Region name (there is no NWR called Northeast Region, see figure 2-5). This leads to confusion in understanding the technical material and leads one to question the conclusions drawn. An example of this errant use of terminology may be found in the "Final Data Set Statistics" on page 38.

11/19/2010 02:48 PM EST 2-4733Chapter 2 - Comment Documents Technical Support Document 

# Comment ID 1296-1.001.005
Author Name: Drew H. Organization: Wood Cellulose Manufacturing Buckeye believes the differences are probably due to several factors. First, in its technical support document ­ Proposed Methods and Approaches for Developing Numeric Nutrient Criteria for Florida Inland Waters, Section 14 ­ EPA reached a conclusion that anthropogenic TN loads should be reduced by 50%, resulting in roughly 30% reduction in TN total load, because Apalachee Bay contains a water body segment (WBID) impaired for nutrients, and typical Florida TMDLs and Pollution Load Reduction Goals recommended average reductions of 36%. This conclusion is inappropriate. There is only one estuarine WBID in all of Apalachee Bay that has been listed for nutrient impairment ­ the Fenholloway River estuary. The remainder of Apalachee Bay has been routinely shown by numerous studies to have excellent unimpaired ecologic health. As such, the presumption that the entire system is impaired due to one small segment, which is already being addressed via the TMDL process, is not appropriate. 

# Response
Comment ID: 0896-1.001.006 Response: EPA recognizes there may be confusion in the naming conventions between EPA’s Nutrient Watershed Regions and a bioregion-based classification. EPA has clarified this in the final rule TSD.
Comment ID: 1296-1.001.005 Response: EPA appreciates the comment regarding downstream protection in Apalachee Bay. EPA has deferred final rulemaking on downstream protection of estuaries to the Agency’s 2011 rulemaking on numeric nutrient criteria for Florida’s estuaries. This decision is consistent with what EPA indicated in its proposed rule signed by the EPA Administrator on January 15, 2010: “At this time, EPA plans to take final action with respect to downstream protection values for nitrogen as part of the second phase of this rulemaking process in coordination with the proposal and finalization of numeric standards for estuarine and coastal waters in 2011” (p. 4208, EPA-HQ-OW-2009-0596, FRL-9105-1). This decision facilitates coordination with the development of proposed estuarine and coastal water quality criteria. EPA will consider these comments as it develops the proposed rule on numeric nutrient criteria for Florida’s estuaries and coastal waters due to be published in November 2011. EPA encourages commenters to consider providing comments on the 2011 proposed rule as part of that rulemaking process, which may reflect modifications to the downstream protection of estuaries approach described in the January 2010 proposed rule for Florida’s inland waters.



# CHAP3 - CHAPTER 3: SPRINGS AND CLEAR STREAMS

11/19/2010 02:48 PM EST 2-4734Chapter 2 - Comment Documents Technical Support Document No Comments are Applicable to this Issue Category, and Thus No Response is Necessary.


# CHAP3A - 3A. BASIS FOR NITRATE-NITRITE CRITERIA Comment ID 1217-2.001.045
Author Name: Voyles J. Organization: Mosaic Fertilizer LLC EPA's technical justification for extending the nitrate criterion from springs and spring runs to clear streams (provided in EPA's Technical Support Document ("TSD") Chapter 3: Methodology for Deriving U.S. EPA's Proposed Criteria for Springs and Clear Streams[43]) does not present a persuasive case for applying the nitrate criteria to clear streams. First, the TSD identifies a correlation between nitrate and algae growth only in relatively open streams (with a canopy cover of forty percent or less) as the basis for applying the spring criteria to streams. It is inappropriate to assume that all clear streams either have an open canopy or could be expected to exhibit an algal response similar to streams with an open canopy. Second, EPA's own statistical analyses show too weak a correlation between nitrate and algal responses to justify extending the nitrate criterion to streams. The analyses contained in Appendix B-11 of the TSD indicate that there is no statistical basis to choose nitrate as the variable having the greatest effect on algal abundance in clear streams.[44] Third, based on the observed relationship, the 0.35 mg/L nitrate criterion is overly protective when applied to clear streams. Appendix B-11 of the TSD shows that the nitrate level consistent with the target level of algae ranges from 1.0 mg/L to 2.0 mg/L.[45] While it may be prudent to set a protective criterion below the concentration associated with impairment, in this case that protective criterion should be nearer the change point of 1.0 mg/L than the proposed criteria of 0.35 mg/L. EPA's own data for clear streams and clear springs with open canopy cover indicate a nitrate criterion much higher than the criterion for springs and spring runs. Accordingly, extending the criteria to clear streams is overprotective and not justified by the data. (A more detailed analysis of EPA's proposed extension of the springs criteria to clear springs is set forth in Attachment 5.) [43] Docket ID: EPA-HQ-OW-2009-0596-0003.3 [44] Docket ID: EPA-HQ-OW-2009-0596-0003.26 [45] Id. 

# Response
Comment ID: 1217-2.001.045 Response: EPA agrees with the comment that applying the springs NO3+NO2 criterion to clear streams is not necessary at this

11/19/2010 02:48 PM EST 2-4735Chapter 2 - Comment Documents Technical Support Document time. EPA has determined that the final TN and TP criteria for streams provide sufficient protection for designated uses in all streams, including clear streams, and therefore, has decided to not apply the additional NO3+NO2 criterion to clear streams. Please see TSD for more detail. 

# CHAP3B - 3B. DURATION AND FREQUENCY FOR PROPOSED SPRINGS CRITERIA No Comments are Applicable to this Issue Category, and Thus No Response is Necessary.


# CHAP3C - 3C. ALTERNATIVE APPROACH CONSIDERED BY U.S. EPA No Comments are Applicable to this Issue Category, and Thus No Response is Necessary.


# CHAP4 - CHAPTER 4: CANALS Comment ID 1352-1.001.164
Author Name: Herr M. Organization: Polk County Data Used to Develop the Criteria A large amount of water quality data from a variety of sources was used in developing the canal standards. Over a million data points from over 2,000 sites were obtained. Agencies contributing data included South Florida Water Management District (SFWMD), FDEP, Broward, and Miami-Dade counties. After a multi-step screening process that removed obvious outliers, records without matching chlorophyll a - nutrient data, mis-labeled entries, etc. a total of 1,622 entries remained and were the basis for the analyses. Of those, 258 had matching chlorophyll a, TN, and TP data. The data were further screened to remove all information from impaired WBIDs. In addition, data from stations in unimpaired WBIDs that were within 1,000 meters of an impaired WBID were excluded. Data from the west region (Big Cypress), the Everglades Agricultural Area (EAA), and the east coast were analyzed separately and together. Some of the data used to derive the canal criterion were taken from canals that were excavated below the soil horizon and extend into the Biscayne aquifer. The Biscayne aquifer is the unconfined surficial aquifer in south Florida and the source of much of the region's potable water. When the water level in the aquifer is higher than the canal water level groundwater will flow into the canal and may significantly affect water quality in the canal. Under these conditions data obtained from sampling canals reflect what is actually the quality of the water in the surficial aquifer, which differs significantly from that of typical surface waters in south Florida. In particular the proposed chlorophyll threshold of 4 ug/L is very low even when compared to chlorophyll concentrations in many relatively unimpaired water bodies. Data from the west coast region (Big Cypress), the EAA, and the east coast region were analyzed separately and together, which provided a reasonable spatial representation for south Florida. About two-thirds of the samples were collected between 1999 and 2009, which covers a wide range of hydrologic conditions.

11/19/2010 02:48 PM EST 2-4736Chapter 2 - Comment Documents Technical Support Document


# Comment ID 1352-1.001.166
Author Name: Herr M. Organization: Polk County The data and information provided by EPA in the Technical Support Documents are not sufficient to fully assess the data and methodologies used. For example, the Access database does not identify which stations were actually included in the final assessment, so it is impossible to attempt to re-create the results stated. In addition, it appears that a significant portion the chlorophyll a data are below the detection limit specified by the lab, but these samples are not identified. The approach of assigning a value of one-half the detection limit to chlorophyll a values that are below the lab specified detection limit is arbitrary. In addition, the target chlorophyll a value of 4 ug/l is within the range of practical quantification limits (PQL) of 3 to 5 ug/l as determined by FDEP audits of several labs, and measured data, as well as below detection limit data, below these values (a significant portion of the total data set) are suspect. 

# Comment ID 1368-1.001.028
Author Name: Waters D. Organization: City of Miami Department of Public Works pg. 4-2 of the TSD divides South Florida based on STATSGO soil types. The entire City of Miami, based on the graphic provided, appears to fall under the category "urban soil". As such, the regional subdivision is useless when considering waterways in the City of Miami and will be of limited utility in highly urbanized areas. The STATSGO database is at too large of a scale to be useful in this analysis, which needs individual canal level resolution. Even the SSURGO database which has resolution on a significantly smaller scale than STATSGO classifies the overwhelming majority of the City of Miami as "Urban Soil". EPA needs to justify why it believes that upland soil characteristics are comparable to aquatic sediment or substrate characteristics for the purpose of classifying canals due to differences of nutrient cycling within the canals. The SSURGO database does not include water features in the same soil classification as the surrounding uplands and does not classify the sediment or substrate located at the bottom of water features. Since STATSGO is an aggregation of SSURGO, EPA did not have any data on the sediment or substrate in the canals, but only on the upland soil types, which calls into question the validity and scientific defensibility of this analysis. It is not unusual for canals to be dredged to hard bottom, or at times to be partly filled. Rather than dividing waterways based on upland soil types which cannot always be determined, use the sub-ecoregions which have already been created by the Florida Department of Environmental Protection. 

# Comment ID 1368-1.001.030
Author Name: Waters D. Organization: City of Miami Department of Public Works

11/19/2010 02:48 PM EST 2-4737Chapter 2 - Comment Documents Technical Support Document pg 4-3 TSD, "Overall, 531 sites were maintained for further analysis, and they include samples collected from 1973through 2009. Approximately two-thirds (64%) of the samples were collected from 1999 through 2009." Given the longterm nature of the samples used to derive the criteria, it is not appropriate to evaluate compliance based on a single year's worth of data. Compliance needs to be evaluated the same way the data were derived - over the long term. Additionally, hurricanes and strong storms can cause a spike in TP and chlorophyll a concentrations since phosphorus tends to sorb to particulates and these are stirred up during strong rain events. Similarly, turbidity may temporarily increase when a canal is dredged. Compliance criteria need to take these factors into consideration. 

# Comment ID 1368-1.001.031
Author Name: Waters D. Organization: City of Miami Department of Public Works Page 4-3 of the TSD states that "994 sites were removed because they were not located in the Everglades Ecoregion". Fig. 5-1 of Proposed Methods and Approaches for Developing Numeric Nutrient Criteria for Florida's Inland Waters depicts 13 Level IV Subecoregions. The Everglades Subecoregion is the central portion of South Florida and extends from Lake Okeechobee in the north to just north of Florida Bay in the south. Fig 5-2 of Proposed Methods document lists Everglades as one of the four (4) Florida Stream Bioregions and seems to be synonymous with the South Florida region delineated by EPA. Should the sentence have read "994 sites were removed because they were not located in the Everglades Bioregion . . ."? The TSD further states that "163 sites were dropped because they were from Lake Okeechobee or nearby canals that might be expected to behave more like a lake than a freshwater canal." From the available figures, it appears that both Lake Okeechobee and nearby canals are included in the Everglades Bioregion. If so, then per the foregoing, the ecoregion needs to be redelineated. If Lake Okeechobee and nearby canals are not included in the Everglades Bioregion, please provide a clearer figure that shows the Bioregion, counties, and waterways. 

# Comment ID 1368-1.001.032
Author Name: Waters D. Organization: City of Miami Department of Public Works Page 4-3 of the TSD ". . . 498 sites were excluded because they were associated with . . . marshes, wetlands . . ." Yet the reference sites for the Bioregion were taken from the Everglades and Big Cypress Subecoregions and pg. 144 of the proposed rule states, "EPA believes that because they [the sites] are remote and surrounded by wetlands [emphasis added], that these canal sites represent sites with the lowest impact from human activities." The 75th percentile values of these wetlands sites for TN, TP, and chlorophyll a were used as an additional line of evidence to justify the numeric nutrient criteria in the proposed rule, yet, according to the technical support document, it appears that they should have been excluded from consideration. Please clarify. 

# Comment ID 1368-1.001.033

11/19/2010 02:48 PM EST 2-4738Chapter 2 - Comment Documents Technical Support Document

Author Name: Waters D. Organization: City of Miami Department of Public Works pg. 4-3 of TSD - upon what basis did EPA decide that values greater than 15 mg/L were erroneous data? Simply because a value is very high does not necessarily mean that it is incorrect or inaccurate. Grab samples are "snapshots" not "average" conditions. Field conditions can be highly variable. Unless samples were collected that violated quality assurance/ quality control protocols or the result is physically impossible, all samples should be included. 

# Comment ID 1368-1.001.034
Author Name: Waters D. Organization: City of Miami Department of Public Works pg 4-4 of TSD - based on EPA's proposal, 25% of non-impaired sites would be flagged as impaired based on the 75th percentile criterion. Though EPA acknowledges that they are not impaired, the rule as currently proposed would classify them as impaired and require the local agencies to propose site-specific alternative criteria or to initiate a TMDL for these unimpaired waterways. EPA, if it decides to determine the surface water quality standard based on a statistical distribution of non-impaired sites, needs to state that the standard does not apply to those sites that were determined not to be impaired and were used to derive the criteria. The rule as proposed also assumes that the waterways which have not yet been assessed for nutrient impairment will overall have a statistically similar response to nutrient concentrations as those which have already been assessed. Please verify that the distribution of the unassessed waterways is not in any way biased (spatially, ecologically, biologically, hydrologically, etc) and that this is a valid assumption. 

# Comment ID 1830.001.031
Author Name: Blair S. Organization: Miami-Dade Department of Environmental Resources Management Comments specific to the Technical Support Document -Chapter 4: Methodology for Deriving U.S. EPA's Proposed Criteria for Canals: TSD Pg. 4-2; Footnote 3: The TSD footnote states the FDEP does not have a record of auditing DERM's laboratory or its contract laboratories. The DERM Laboratory has been audited by multiple state agencies, including annual NELAP audits, and generally biannual audits by the South Florida Water Management District. Additionally, the Lab was audited by FDEP in 1997, and, as noted in Footnote 3, has been a consistent participant in the State's ‘Everglades round robin inter-laboratory phosphorus comparability' exercises. 

# Comment ID 1830.001.032

11/19/2010 02:48 PM EST 2-4739Chapter 2 - Comment Documents Technical Support Document

Author Name: Blair S. Organization: Miami-Dade Department of Environmental Resources Management TSD Pg. 4-3; Bullet 1 The document states that 88 sites were ‘dropped' as "...more than 5% of the specific conductivity results were greater than 3,000 uS/cm; ...". The basis for this determination is not clear. There a multiple programs throughout the region with varied sample-site protocols and may collect data at different, or multiple depths. The conductivity of importance is that where the concordant nutrient sample was taken. When assessing the conductivity of a ‘station', it is recommended that only the conductivity which corresponds to the depth at which the nutrient sample was collected be considered. The presence of a salt-wedge may result in ‘averaged' values being greater than 3,000 uS/cm, despite the fact that the nutrient sample (and resultant data) were taken from a freshwater portion of the water column. 

# Comment ID 1834-4.001.025
Author Name: Bronson C. Organization: Florida Department of Agriculture and Consumer Services 4. Proposed Criteria are Overly Protective of Many Areas of South Florida due to EPAs Failure to Develop Different Criteria for the Four Distinct Geologic Regions The Technical Support Document (TSD) supporting criteria development for canals states: “Because soil or substrate type at the bottom of the canal can influence the nutrient cycling and relationships between the observed biological response and the TP and TN)levels in canals, U.S. EPA used data on soil types in South Florida, along with knowledge of the Everglades Agricultural Area (EAA) and the Everglades Protection Area (EvPA), to subdivide the canal areas for criteria derivation (see Figures 4-1a and 4-1b). Thus the first step in this and other analyses was to group canals and canal data by soil type. The four groupings are the histosol and entisol soils of the EAA; histosol and entisol soils of the EvPA; spodosol and alfisol soils and areas west of the EvPA and EAA (hereafter, West Coast); and spodosol, entisol, and alfisol soils and areas east of the EvPA and EAA (hereafter East Coast).” Statistical analyses in the TSD were all conducted unique to each canal region. When the criteria were developed, however, data for all regions were all combined into a single category (data for the EvPA were excluded from calculation of the TP criterion, due to the existence of a numerical criterion), resulting in arbitrary criteria. Because EPA recognizes that soil types are important drivers for resulting nutrient concentrations, the criteria development should be unique to each different soil type. A specific example of the need to develop distinct criteria for each soil type is exemplified by the proposed TN criterion for EAA canals. In 2007 EPA stated, “EPA is unaware of any data indicating that nitrogen causes imbalances in flora or fauna in Class III canals within the EAA.” [xi] Since EPA failed to provide any evidence to the contrary or alter their previous conclusion it is arbitrary to propose a TN criterion for the EAA canals. In summary, no scientific basis is presented to establish uniform criteria for Florida canals. EPA needs first to establish goals for conditions it seeks to protect in establishing nutrient criteria for canals, and it must develop a rational basis for classifying canals according to these goals. EPA needs to determine what response variables are appropriate to indicate that those conditions are being protected and determine appropriate threshold values of the indicators related

11/19/2010 02:48 PM EST 2-4740Chapter 2 - Comment Documents Technical Support Document to impairment of the intended uses or aquatic life conditions to be protected. Finally, it needs to establish reliable relationships between threshold indicator values and nutrient concentrations. EPA unfortunately has done none of these steps in the Chapter 4 document, and consequently the proposed nutrient criteria are arbitrary and should not be implemented.


# Comment ID 2233-1.001.096
Author Name: Kovach C. Organization: CF Industries Aside from these concerns, several specific technical issues and shortcomings were found in the report, as described below. Use of the 75th percentile is arbitrary and does not represent the use of sound science. This arbitrary approach could lead to under-protection or over-protection, and it is not possible to evaluate which is more likely. From comments made by USEPA in the second paragraph on page 2, it appears that EPA is acknowledging that the proposed criteria based on 75th percentile values cannot be defended as representing threshold values for impairment of aquatic life or intended uses in canals. 

# Comment ID 2233-1.001.098
Author Name: Kovach C. Organization: CF Industries The period of record used for the data base is too long ( > 35 years). For purposes of data comparability, the EPA should have used just the two-thirds of the data from 1999-2009. Analytical methods and reliability of data have changed substantially over the period of record. Environmental conditions also have changed. Inclusion of data from such a long period leads to greater heterogeneity in the data base, making it more difficult to analyze and more difficult to defend. 

# Comment ID 2233-1.001.106
Author Name: Kovach C. Organization: CF Industries In summary, the EPA has presented no scientific basis to establish nutrient criteria for Florida canals. If numeric nutrient criteria are to be developed for canals, the EPA will need first to establish goals for the conditions it seeks to protect by establishing nutrient criteria for canals. To do this properly, it must develop a rational basis for classifying canals according to their uses and these goals. The EPA needs to establish appropriate response variables indicate that those conditions are being protected, and it needs to determine appropriate threshold values of the indicators related to impairment of the intended/designated uses or aquatic life conditions that are to be protected. Finally, the EPA needs to

11/19/2010 02:48 PM EST 2-4741Chapter 2 - Comment Documents Technical Support Document establish reliable and defensible relationships between the threshold indicator values and nutrient concentrations. Unfortunately, the EPA did none of these steps in the Chapter 4 document. Consequently, the proposed nutrient criteria should not be implemented 

# Response
Comment IDs: All Response: EPA acknowledges the issues raised by the commenters related to numeric nutrient criteria for flowing waters in South Florida, particularly regarding segmentation, delineation, data selection, analysis procedures including use of the reference approach, chlorophyll method detection limits, and assessment periods. EPA has deferred rulemaking on numeric nutrient criteria for flowing waters in South Florida to 2011. EPA will propose numeric nutrient criteria for Florida’s estuarine and coastal waters, including inland flowing fresh waters in South Florida, by November 14, 2011. EPA will consider these comments as it moves forward in developing the Agency’s proposed rule. EPA encourages commenters to review the Agency’s proposed rule at that time and to submit comments regarding inland flowing fresh waters in South Florida. 

# CHAP4A - 4A. OTHER ANALYSES CONDUCTED AND CONSIDERED BY U.S. EPA IN THE DERIVATION OF PROPOSED NUMERIC NUTRIENT CRITERIA FOR CANALS Comment ID 0896-1.001.009
Author Name: * * Organization: Lee County Division of Natural Resources Chapter 4: Methodology for Deriving U.S. EPA's Proposed Criteria for Canals The nitrogen criterion relies on concentration and does not consider flow. Physical factors that influence nitrogen loading and the presence of chlorophyll-a are important to consider for downstream protection particularly given that canals are primarily built to move water off of the land seasonally. They are typically not built to with nutrient assimilation as a priority function. The evaluation for phosphorus does however include loading rather than relying only on concentration and as with most water quality data collected in freshwater portions of South Florida seems to be better understood, however STAs are built with nutrient assimilation as a priority function and using STAs to build assumptions for canal functionality may under-estimate loading that canals will contribute to downstream waters.

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# Comment ID 1232.001.001
Author Name: Parsons P. Organization: Florida Sugar Cane League I'm Philip Parsons, speaking again for the Florida Sugar Cane League. And I appreciate this additional opportunity for comments. Time permitting, I want to make three points relating to your technical support document used to derive criteria for the South Florida canals. I won't address streams or lakes or water bodies throughout the rest of the state. In that document, your technical support document, you analyze the various regions in South Florida and identify four subregions based on soils, geology, and hydrologic factors that justify separate criteria for each region. And it may surprise you to know that we agree with that analysis and your assessment. The problem we have is you don't use that. You then ignore the subregional groupings and derive a criteria that will apply to all, four very different regions that are as different between them as the differences between Bone Valley and other parts of Florida. We think if you take that approach, you will have broad-based support for subregionalization. We think if you derive criteria separately for each region, you'll have increased support for the criteria for those canal systems. It's an opportunity to solve several problems. The -- I commented earlier on the unique characteristics of the Biscayne Aquifer. Today I'll focus primarily on the Everglades agricultural area, which is the large region of organic soils in which the Florida Sugar Cane League and other farmers are engaged in agricultural activities. These are nitrogen-rich soils, and they are the primary source of nitrogen to the canals and in water leaving that system. Farmers add insignificant amounts of nitrogen as fertilizer and only on a few crops. Very little nitrogen is added, and it is insignificant. You, though, have excluded almost all the nitrogen data that's available from the E.A.A. in your derivation of nutrient criteria for South Florida canals. You have excluded those, we assume, because this is not explained fully in your technical support document, we assume you have excluded those because Department of Environmental Protection concluded that dissolved oxygen is depressed in the E.A.A. and nutrients may be a factor in causing that. Even if that's so, that's not an adequate basis for excluding the data regarding nitrogen. We are not arguing against numeric nutrient criteria for nitrogen in the E.A.A. or anywhere else, but we believe you ought to use the available data that's appropriate for that area. And we think what we're proposing is consistent with your own conclusions earlier when you proposed the T.M.D.L. for the Everglades in September of 2007. And you concluded in that document that phosphorus is clearly the issue in both

11/19/2010 02:48 PM EST 2-4743Chapter 2 - Comment Documents Technical Support Document the E.A.A. canals and in the Everglades. You say that because the Everglades marsh is phosphorus limited, nitrogen hasn't been a concern in the Everglades. There is no numeric water quality criterion for total nitrogen in the Everglades.
E.P.A. is unaware of any data indicating that nitrogen causes imbalances in flora or fauna in the Class III canals in the E.A.A. We agree with that conclusion. And if that is a sound conclusion, it's inconsistent to determine that those canals are impaired for nitrogen. I'm not addressing phosphorus, I'm addressing nitrogen. And in almost every case, it's the link with the O, the potential contribution of nitrogen. And you say further, you conclude further in the same T.M.D.L. document that E.A.A. WBIDs that are impaired, are listed as impaired for dissolved oxygen, D.L. may be depressed by excess nutrients, it may also be expressed in canals due to groundwater influence. And I can assure you that groundwater influence in the E.A.A. is a major, not the exclusive factor, but a major influence on dissolved oxygen. I won't continue with other statements that you made in that T.M.D.L., we'll do this in writing. But your assessment in 2007 is consistent with what we are proposing. Thank you. 

# Comment ID 1688-1.001.003
Author Name: Brooks J. Organization: Florida Department of Environmental Protection Geographic Areas of South Florida and the Trophic Expectation of those Regions EPA's technical support documents subdivided South Florida into four Regions (see Chapter 4 of EPA's Technical Support Document): Because soil or substrate type at the bottom of a canal can influence the nutrient cycling and relationships between the observed biological response and the total phosphorus (TP) and total nitrogen (TN) levels in canals, U.S. EPA used data on soil types in south Florida, along with knowledge of the Everglades Agricultural Area (EAA) and the Everglades Protection Area (EvPA), to subdivide the canal areas for criteria derivation (see Figures 4-1a and 4-1b). Thus the first step in this and other analyses was to group canals and canal data by soil type. The four groupings are the histosol and entisol soils of the EAA; histosol and entisol soils of the EvPA; spodosol and alfisol soils and areas west of the EvPA and EAA (hereafter, West Coast); and spodosol, entisol, and alfisol soils and areas east of the EvPA and EAA (hereafter East Coast). Soil types and geology can greatly influence the water chemistry of a waterbody and these geographic distinctions may be appropriate for South Florida canals. Current ambient water quality characteristics for nutrients for these four Regions are calculated by the South Florida Water Management District and submitted with their comments. 

# Comment ID 1830.001.017

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Author Name: Blair S. Organization: Miami-Dade Department of Environmental Resources Management 10. It is recommended that the criteria be evaluated and applied on a ‘subarea' basis similar to, but even more specific than, the approach described in EPA TSD (Ch 4 & 4a). A single criterion is not appropriate for application all canals in Southern Florida. Even the "East Coast" region described in Ch 4 is too large in geographic scale. It is suggested that minimally, the "East Coast" be further subdivided on a ‘Watershed' approach, wherein canals are aggregated within the regional drainage areas, considering hydrology, substrate, and other geochemical factors. Criteria should be developed and applied to the identified areas using a regional/watershed approach (i.e., Biscayne Bay, Broward-ICW/Lake Worth Lagoon). This is similar to the approach used for "Streams" and "Springs, spring runs and clear streams" (Section C(1)). 

# Comment ID 2233-1.001.094
Author Name: Kovach C. Organization: CF Industries The EPA also described a series of alternative approaches it considered and presented results from those analyses. Section 4.a describes an approach using canals near Highway 41 in South Florida (between the Everglades Protection Area and Big Cypress Swamp) as "reference canals." Based on a statistical analysis of data from these canals, criteria are presented, without comment or discussion, for TP, TN, and chlorophyll a. No comparison was made with the values developed by the first method, and no reasons were given for not using these values instead of those derived by the first method. 

# Comment ID 2233-1.001.097
Author Name: Kovach C. Organization: CF Industries The maps in Figure 4-1 provide no evidence that the soils of the EAA and EvPA are inherently different. In addition, is it not clear from the maps of soil orders that the soils on the east and west coasts are inherently different from each other. Rather than using a geographic classification, the USEPA should have grouped canals in similar soil types on the east and west coasts and in the two Everglades regions together. 

# Comment ID 2233-1.001.099
Author Name: Kovach C. Organization: CF Industries The nutrient and chlorophyll numbers presented on p. 4 do not make sense in that the chlorophyll a concentration is

11/19/2010 02:48 PM EST 2-4745Chapter 2 - Comment Documents Technical Support Document very low relative to the TN and TP concentrations. In fact, the chlorophyll a concentration (4.0 ug/L) is lower than the value associated with unimpaired water quality conditions in natural surface waters. The chlorophyll limit that the EPA used for alkaline lakes is 20 ug/L, a factor almost 5x higher. As a result, the associated nutrient concentrations of 1.6 mg/L (TN) and 0.042 mg/L (TP) would not appear to be appropriate as nutrient criteria for canals. 

# Comment ID 2233-1.001.100
Author Name: Kovach C. Organization: CF Industries Use of the 25th percentile as the criterion (p. 4, bottom line) has no scientific basis and is arbitrary. Why EPA would propose such an approach, particularly in South Florida, where nearly all canals are affected by human activity, is difficult to understand. 

# Comment ID 2233-1.001.101
Author Name: Kovach C. Organization: CF Industries Page 5. The use of TN values is as inappropriate for canals as it is in the development of nutrient criteria for lakes and streams: in Florida a large but variable fraction of the TN is tied up in dissolved humic matter and is biologically unavailable. 

# Response
Comment IDs: All Response: EPA acknowledges the issues raised by the commenters related to segmentation, data selection, analysis procedures including use of the reference approach, and the magnitude of the proposed chlorophyll criteria with regard to flowing waters in South Florida. EPA has deferred rulemaking on numeric nutrient criteria for flowing waters in South Florida to 2011. EPA will propose numeric nutrient criteria for Florida’s estuarine and coastal waters by November 14, 2011. At that time, EPA will also repropose numeric nutrient criteria for inland flowing fresh waters in South Florida. EPA will consider these comments as it moves forward in developing the Agency’s proposed rule. EPA encourages commenters to review the Agency’s proposed rule at that time and to submit comments regarding inland flowing fresh waters in South Florida. 

# CHAP4B - 4B. DURATION AND FREQUENCY FOR PROPOSED CANALS CRITERIA

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# Comment ID 1715-3.001.027
Author Name: Wilson C. Organization: Gunster, Yoakley & Stewart, P.A. on behalf of Everglades Agricultural Area Environmental Protection District Inability to Duplicate USEPA Calculations/Inconsistencies in Data Summaries Dilks (2010) conducted an independent statistical assessment of the canal water quality data provided by USEPA. Results of that analysis yielded different values than those provided in Chapter 4 of USEPA's Technical Support Document (USEPA 2010a). Furthermore, the data summaries provided by USEPA in Tables 4-1 and 4-2 of this document contain internal inconsistencies. Using USEPA's own procedures, queries were used in Microsoft Access to create Region-WBID-Year records that aggregate TP, TN, and chlorophyll results. These were exported to Excel and processed to calculate (for unimpaired stations only) the mean and standard deviation of the log-transformed TP, TN and chlorophyll in each of the four regions and for the entire set of records. The results of these calculations were compared to the values presented in Table 4-1 of the TSD, and were found to match exactly - but only in cases where the counts of records matched. There were differences between the Table 4-1 counts of WBID-Years and our independent counts for two of the five tabulated chlorophyll rows, four of the TN, and two of the TP rows. In addition, the number of WBID-Year records presented for all regions in Table 4-1 is less than the sum of WBID-Year records for all regions. The WBID-Year counts that we calculated are listed in Table 2 and compared with the values presented by the TSD. Original comment letter contains additional informaiton in Table 2. Discrepancies WBID-Year Count between EPA Table 4-1 and Independent EAA/EPD Calculation (from Dilks 2010). See original comment letter. 

# Response
Comment ID: 1715-3.001.027 Response: EPA thanks the commenter for their review of the analyses. EPA has deferred rulemaking on numeric nutrient criteria for flowing waters in South Florida to 2011. EPA will propose numeric nutrient criteria for Florida’s estuarine and coastal waters, including inland flowing fresh waters in South Florida, by November 14, 2011. EPA will consider these comments as it moves forward in developing the Agency’s proposed rule. EPA encourages commenters to review the Agency’s proposed rule at that time and to submit comments regarding inland flowing fresh waters in South Florida. 

# CHAP4C - 4C. ALTERNATIVE APPROACH CONSIDERED Comment ID 0896-1.001.010

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Author Name: * * Organization: Lee County Division of Natural Resources Chapter 4: Methodology for Deriving U.S. EPA's Proposed Criteria for Canals Overall it appears that water quality criteria that are being developed for the South NWR is relying completely on canal data. In fact, there are numerous stream systems in the South NWR that are naturally occurring and that do not function like canals. To date DEP has not developed stream condition indexes that are applicable south of the Caloosahatchee Basin. Biological criteria for the South NWR should be developed for natural stream systems prior to adopting a blanket criteria based on canals. 

# Comment ID 1368-1.001.027
Author Name: Waters D. Organization: City of Miami Department of Public Works Technical Support Document Line Item Comments From EPA Ch 4 TSD, it appears that samples were included from Miami Canal Watershed per Fig. 4-5 on pg 4-16. The Florida Department of Environmental Protection classifies the Miami Canal as an estuary. Please verify that these were fresh water samples. 

# Comment ID 1474-1.001.074
Author Name: Herz W. Organization: The Fertilizer Institute 4. EPA proposes to regulate canals with no evidence of nutrient impairment. The data plots presented in EPA's TDS show that virtually all of canals assessed have chlorophyll a levels less than 20 ug/l. See TSD at 4-17 to 4-19. It appears that over 90 percent of the data points are below 10 ug/l. From this information, it is not apparent that any long term average chlorophyll a levels would exceed 10 ug/l. Such water quality is generally considered excellent for protecting aquatic life uses. Moreover, these data do not indicate that canals have any nutrient impairment problems. Mesotrophic levels are met in all of these waters on an individual year basis and oligotrophic levels are met on a long term average basis. EPA has concluded that both of these levels are protective of aquatic life elsewhere in the State. Given this information, EPA should not have determined that it was necessary to set canal nutrient standards or that Florida's actions were insufficient to protect such waters. 

# Comment ID 1830.001.015

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Author Name: Blair S. Organization: Miami-Dade Department of Environmental Resources Management 8. The EPA TSD, Chapter 4 states that the quartiles for the entire south Florida region were derived based on the distribution of the annual arithmetic means of the natural log of the data aggregated by WBID-year (i.e., data from 1 or more sites within a defined water body segment [e.g., a WBID] were aggregated together, and summarized as annual means (e.g. "WBID-Years"). Thus the criterion is based on the distribution of aggregated data across all of South Florida. This ignores subregional variability in site conditions that can affect nutrient concentrations. For example, a differentiation of limiting nutrients on the west coast of Florida, versus the East Coast of Florida has been documented (RECOVER, 2010. CERP 2009 SSR (draft). fig.9-48). Whereas eastern canals have very low levels of Phosphorus (TP) and relatively higher levels of Nitrogen (TN), western canals have significantly higher TP concentrations, and relatively lower TN concentrations. Aggregating data from all south Florida canals effectively skews the quartile assessment to the produce elevated TP criteria for the eastern canals, and elevated TN criteria for the western Canals. 

# Comment ID 1834-4.001.031
Author Name: Bronson C. Organization: Florida Department of Agriculture and Consumer Services 2. The "Upper Percentile Criterion with Low Exceedance Frequency" considered by EPA will result in an unacceptably large percentage of unimpaired sites being considered as impaired; 

# Comment ID 1834-4.001.033
Author Name: Bronson C. Organization: Florida Department of Agriculture and Consumer Services 1. EPA’s alternative canal criteria based on the 25th percentile of all canal data has an unacceptably high false positive rate Surveys of South Florida canals and data from FDEP and DERM using the SCI technique consistently have shown that macroinvertebrate communities are of poor quality, over a wide range of nutrient concentrations, due to habitat limitations. Because of the lack of this relationship between nutrient concentration and environmental response, no threshold concentration could be identified that would be protective of designated uses. Healthy balanced populations of flora and fauna occur in both oligotrophic and eutrophic systems, despite differences in the ambient nutrient concentrations. Models relating biological condition to human disturbance gradients across different water bodies suggest that the aggregate impact of multiple stressors can result in a measurable difference in biological assessment scores, when compared to water bodies with minimal disturbance. It is unclear, however, how individual systems will respond to reductions in nutrient levels over time, when a variety of factors influence biological health. Attainment of the proposed numeric nutrient criteria therefore offers no reasonable assurance that the designated use will be met in the

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non-reference waterbodies. The false positive rates associated with the 25th percentile estimates given in Table 4-2 of the TSD are unacceptably high. This is not surprising since the across region limits are drastically reduced to 2.1 ug/L for chlorophyll, 1.08 for TN mg/L, and .018 mg/L for TP. Assuming an unimpaired site is sampled eight times per year; the frequency and durationtests applied to the 25th percentile limits produce a false positive rate of at least 90%. It was assumed that the longterm mean would be calculated over seven years, although shorter or longer duration specifications yield similar results.


# Comment ID 1834-4.001.034
Author Name: Bronson C. Organization: Florida Department of Agriculture and Consumer Services 2. The “Upper Percentile Criterion with Low Exceedance Frequency” considered by EPA will result in an unacceptably large percentage of unimpaired sites being considered as impaired. In the Numeric Rule Section entitled “Other Data and Analyses Conducted and Considered by EPA in the Derivation of the Proposed Numeric Nutrient Criteria for South Florida Canals”, EPA calculates an “Upper Percentile Criterion with Low Exceedance Frequency”. The purpose of this analysis is to compute a “not to exceed” concentration for a single sample for a station that meets both the duration and frequency tests. The “Not to Exceed” values could not be exactly replicated. Assuming that EPA correctly calculated the additional criterion and the false positive rate for a given site and sampling date is 5% when the site meets the duration and frequency tests, the false positive rates for these sites increase dramatically as a function of sampling frequency as noted in Table 2 and Figure 5 below: Original comment letter contains additional information for canals from FDEP in Table 2. False Positives as a Function of Sampling Frequency. See original comment letter. Original comment letter contains additional information for canals from FDEP in Figure 5. Probability of At Least One Sample Exceeding the Single Sample Maximum Criterion for a Site Exactly Attaining the Water Quality Criterion. See original comment letter. At a sampling frequency of once/week, there is almost a 100% chance that the site will be declared in exceedance during the year. It is inappropriate for EPA to consider a single sample test for sites that pass the annual frequency and duration tests. The single sample limits given in Table 4-4 are calculated assuming the mean of the distribution is at the proposed annual geometric mean criterion, e.g. 1.6 mg/L for TN. Assuming instead the statistical distribution of an unimpaired site (as defined by the sites used in Table 4-1) and if the site is sampled weekly, then the chance of declaring a single sample to be in exceedance at least once during the year adds a minimum of 10% to the annual false positive rate of TP and TN. Of course, this additional rate depends upon the sampling frequency and parameter of interest. The results presented in Table 4-4 for chlorophyll are not reproducible from the data provided by EPA and therefore are arbitrary.

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# Comment ID 2233-1.001.095
Author Name: Kovach C. Organization: CF Industries The report also describes the development of nutrient criteria based on a "stressor-response" approach (p. 4-6, Section 4c.i), in which TP and TN data were regressed against chlorophyll a data. TP and TN criteria were developed from the regression relationships using a target chlorophyll value of 20 ug/L.The line of best fit between In TP and In chl a (or between In TN and In chl a) was not used to establish the criteria, and instead EPA used a line representing the 90% confidence interval for the relationship. Why this value was selected was not explained or justified,, and the report does not explain how (or whether) intended/designated uses of canals or their ecological health would be impaired at higher chlorophyll concentrations. No discussion is provided regarding the quality of the relationships or accuracy/reliability of the calculated results as nutrient criteria; no comparison was made with the criteria values developed by the earlier methods; and no reasons were given for why these values were not used to establish the nutrient criteria instead of those derived by the earlier methods. Similarly, two other approaches were described in later sections of the document, and in each section there is a lack of comparison of results from the different methods and a lack of any statements about the appropriateness of the criteria developed by the method. In the end, the reader is left with the feeling that none of the methods was considered to be a valid way to develop nutrient criteria for Florida canals. 

# Comment ID 2233-1.001.103
Author Name: Kovach C. Organization: CF Industries A value of 20 ug/L for chlorophyll was used to compute apparent TP criteria from the regression relationships, but no foundation is laid that this value is an appropriate limit for chlorophyll in canals. Consequently, it is not possible to interpret the TP values calculated by EPA from the regression relationships as valid nutrient criteria. 

# Comment ID 2233-1.001.104
Author Name: Kovach C. Organization: CF Industries The chlorophyll-TP regressions show considerable scatter, and less than half of the variance in chlorophyll is explained by the regressions. In addition, only one or two of the data points shown in Figure 4-6b equal or exceed 20 ug/L for chlorophyll; this adds additional uncertainty to the extrapolation of an associated TP concentration. It is not clear why the EPA chose a 90% confidence level as the basis for calculating the TP concentration rather than the value associated with the regression line itself (the line of best fit). A value of 75% confidence was used by EPA to develop lake nutrient criteria.

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# Comment ID 2233-1.001.105
Author Name: Kovach C. Organization: CF Industries The regression analyses for chlorophyll versus TN show essentially no useful relationships. The low r2 values indicate that only a very minor portion of the variance in chlorophyll is explained by TN. No useful (or defensible) criteria can be developed for TN from these regressions. 

# Response
Comment IDs: All Response: EPA acknowledges the issues raised by the commenters related to segmentation, presence of natural streams, scientific basis, analysis procedures, data selection, analysis procedures including use of the reference approach, and the magnitude of the proposed chlorophyll criteria with regard to flowing waters in South Florida. EPA has deferred rulemaking on numeric nutrient criteria for flowing waters in South Florida to 2011. EPA will propose numeric nutrient criteria for Florida’s estuarine and coastal waters by November 14, 2011. At that time, EPA will also repropose numeric nutrient criteria for inland flowing fresh waters in South Florida. EPA will consider these comments as it moves forward in developing the Agency’s proposed rule. EPA encourages commenters to review the Agency’s proposed rule at that time and to submit comments regarding inland flowing fresh waters in South Florida. 

# APPNDX-A - APPENDIX A: SUPPORTING AND EXPLORATORY ANALYSES FOR LAKES Comment ID 0896-1.001.005
Author Name: * * Organization: Lee County Division of Natural Resources Appendix A-8: FDEP's Benchmark Lake Summaries The summaries should include what eco-region they are located within to give the reader some context to go with the description of the physical and chemical attributes. 

# Response

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Comment ID: 0896-1.001.005 Response: EPA has considered the comment suggesting that lake benchmark summaries should include ecoregional information. EPA did not base its lake criteria on lake benchmark information and thus chose not to include ecoregional information as suggested. 

# APPNDX-B - APPENDIX B: SUPPORTING AND EXPLORATORY ANALYSES FOR STREAMS AND CANALS Comment ID 1011.001.004
Author Name: Todd, Jr. K. Organization: Palm Beach County The following points are made concerning the technical aspects of the proposed rule: 1) There is a discrepancy between the map showing the watersheds and drainage areas that represent the Peninsula Region and the text on pages 72 and 189 within the rule that describes the mapped areas. The graphic map (Appendix B-1) identifies that the Peninsula Region extends into Palm Beach County. The text needs to be modified to include the Loxahatchee Watershed, the L-8 Basin, the C-18 Basin, and the Palm Beach County Northeastern Coastal Basin so it is consistent with the areas shown on the map. 

# Comment ID 1292-1.001.051
Author Name: Wiegand P. Organization: National Council for Air and Stream Improvement, Inc. Methods According to Appendix B-1 of the EPA Technical Support Document (TSD) for the proposed criteria (docket file EPA-HQ-OW-2009-0596-0003.16.pdf), methods of data collection for the RPS dataset followed procedures detailed in DEP-SOP-001/01 FS 7130. For this evaluation, average algal thickness was rank-ordered and divided into four quartiles after removing records with no algal thickness measurement. To identify general tendencies between algal thickness quartiles and other variables in the dataset, summary statistics and box plots of the levels of explanatory variables associated with each algal thickness quartile were used. The explanatory variables included stream shading (represented as average percent canopy cover), stream color, turbidity, specific conductance, pH, several nutrient variables including TP and TN, and others. Summary statistics for these variables are provided in Table 4.1. Original comment letter contains additional information for streams and rivers in Table 4.1. Summary Statistics for Average Algal Thickness and Several Candidate Explanatory Variables for Each of the Four Algal Thickness Quartiles from the comment report of the National Council for Air and Stream Improvement, Inc. (NCASI) relating to EPA's January 26, 2010 proposal of numeric nutrient water quality criteria for lakes and flowing waters in the State of Florida. See original comment letter.

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# Comment ID 1292-1.001.074
Author Name: Wiegand P. Organization: National Council for Air and Stream Improvement, Inc. Comparison with Findings of the EPA/FDEP Technical Support Document The analysis presented above is exploratory and is not intended to provide a comprehensive assessment of the RPS dataset. Additional data exploration and more detailed statistical analysis could reveal additional patterns, including those indicative of nutrient pollution, that may be used to improve management of nutrient-related concerns. Appendices B-1 and B-11 of the EPA TSD present a more detailed evaluation of the RPS dataset using several statistical procedures. One component of the analysis focuses on the "abundance of algae in streams," and its principal findings can be compared with the information presented above. Results of a statistical correlation analysis are presented in Table B1-3. Some quotations from the text associated with this part of the analysis include: "The analyses indicated that canopy cover, color, pH, total Kjeldahl nitrogen, organic nitrogen, and nitrate- nitrite were the factors most highly correlated to algal thickness. The strong correlations with color and canopy cover were expected since they can cause light limitation and therefore directly reduce periphyton growth. The relatively strong correlations between pH, TKN, and organic nitrogen and algal biomass were unexpected, but can likely be explained by their strong correlations with color (Spearman correlations were 0.79, 0.80, and -0.52, respectively)." "As shown in Figure B1-3, periphyton thickness appears to be significantly correlated with nitrate- nitrite, canopy cover, and water color, but not with TP. It should be noted that color is a strong confounding factor in these analyses since it is correlated to some extent with canopy cover, nitrate-nitrite concentration, and TP concentration." This is consistent with the findings of the average algal thickness quartile analysis presented here. The associations between TP and TN and algal thickness are weak or non-existent, while the strongest associations involve canopy cover, stream color, and, among nutrient species, nitrate-nitrite. Whether decreasing canopy cover or color or increasing nitrate-nitrite are more important in causing increases in algal cover is unknown. TKN is primarily comprised of organic N, so associations involving one of these two variables would also be true of the other. In addition, both the quartile analysis and Table B1-3 in Appendix B-1of the EPA TSD make clear that the association between TKN and algal thickness is negative, not positive (Table 4.2) and probably corresponds to the observation that organic nitrogen tends to increase with increasing color. Regarding the potential impact on algal thickness, color appears to be the more dominant of the two variables. Original comment letter contains additional information in Table 4.2. Spearman Rank Correlation Coefficients between Mean Algal Thickness and Nutrient Variables Listed in Table B1-3 in Appendix B-1 of the EPA TSD [correlation coefficients for canopy cover and color are provided for reference]) for streams and rivers from the comment report of the National Council for Air and Stream Improvement, Inc. (NCASI). See original comment letter.

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# Comment ID 1292-1.001.076
Author Name: Wiegand P. Organization: National Council for Air and Stream Improvement, Inc. The document then describes an analysis of relationships after dividing streams into three color classes: clear (<40 pcu), intermediate (40 to 100 pcu), and high (>100 pcu). The report states: "The relationships between nutrients and periphyton thickness were much stronger in clear streams (FigureB1-4 a1-a3) than in colored streams (Figure B1-4 c1-c3), indicated by the stronger spearman correlations as well as improved LOESS regressions in the clear streams. The main relationships observed were between nitrogen parameters and benthic algal thickness. The effect of phosphorus did not appear to be significant in these analyses. Where color is increased (increased potential for light limitation), nutrients do not exert as important a role in algal biomass accumulations." A summary relating to algal thickness from the more detailed data analysis provided in Appendix B-11 states: "a. Algal thickness was strongly light limited in most Florida streams, and was limited by both forest canopy cover and water color; b. Algal thickness was strongly correlated with color, a factor that potentially led to light limitation but also released algae from nutrient limitation since higher color was associated with higher nutrient concentrations;

c. The only nutrient variable that was significantly correlated with algal thickness was NO2+3 concentration. However, this correlation was confounded by the correlation between color and algal thickness; in other words, colored streams had both lower NO2+3 concentrations and reduced algal thickness compared to clear streams." One important observation from the above statements is that neither TP nor TN are likely to be reliable indicators of algal thickness, even in clearer waters, in spite of broad references in Appendix B-1 to "relationships between nutrients and periphyton thickness" as being "stronger" in these streams. In addition, item c indicates that color and nitrate-nitrite are negatively correlated (i.e., higher color is associated with lower nitrate-nitrite) and that it is unknown whether decreasing color, increasing nitrate-nitrite, both, or neither are causes of higher observed algal thickness. It has been noted that algal thickness is not a strong determinant of 45 macroinvertebrate quality (measured as SCI score) over the range of values typical of the RPS dataset. In addition to an evaluation of algal thickness, Appendix B-1 of the EPA TSD describes evaluations of the chlorophyll a data in the RPS dataset and states: "An analysis was also conducted to evaluate the relationship between nutrients and phytoplankton chl. a collected for the same sites. In contrast to algal biomass data, the relationships between phytoplankton chl. a and nutrients were much stronger in colored streams (FigureB1-5 b1-c3) than in clear streams (FigureB1-5 a1-a3), especially between total nitrogen and chl. a concentrations. The Spearman correlations between chl. a and total nitrogen were 0.36 and 0.42, respectively, in intermediate and high color streams, but was -0.16 in clear streams. With the increased color and

11/19/2010 02:48 PM EST 2-4755Chapter 2 - Comment Documents Technical Support Document stronger light limitation to periphyton, phytoplankton appear more able to utilize the available nutrients than periphyton. Chl. a appeared to respond somewhat to phosphorus, but all of the responses were statistically weak. The general use of the term "nutrients" in the above quote and elsewhere in the document is problematic. This term might be construed to refer to all forms of nutrients and in particular the forms for which criteria have been proposed, namely TP and TN. In fact, as made clear upon more detailed review of Appendix B-1, "nutrients" typically refers to certain chemical species and generally does not include TP. A number of conclusions in Appendix B-1 appear to be based on Spearman correlation coefficients. It should be noted that while the Spearman correlation procedure appears to correctly indicate the generally weak nature of the relationships in these data, it is poorly suited to characterizing many of the associations described in this chapter and its appendices. It is best used to describe monotonic relationships between two variables; that is, relationships that tend to follow a straight line or have a curve in one direction (Helsel and Hirsch 2002). Many of the scatter plots shown inAppendix B11 with associated Spearman correlation coefficients (e.g., Figures B11-4 and B11-5) appear to doubleback on themselves, and therefore are not monotonic. This limits the value of the information presented on Spearman correlation coefficients as evidence of meaningful relationships between nutrient species and aquatic plant growth or for making comparisons between nutrient variables. The TSD also evaluates the possibility that nitrogen and phosphorus could be co-limiting, potentially masking the effect of TP on algal biomass, especially in clear streams: "As indicated in Figure B1-6 d-e, the combined nutrient variables have a stronger correlation to algal thickness than the individual nutrient concentrations, potentially indicating N and P co-limitation for some streams. This finding also indicates that both nitrogen (TN and NOx) and phosphorus are significant in controlling algal thickness in streams. More details concerning these analyses are provided in Appendix B-11." Figure B1-6 is not of all streams, but rather is a subset of streams with "transect canopy <=40% and color <=40 pcu." Thus the effect described apparently does not apply to more shaded, colored streams. The conclusions of Appendix B1, referring to all the analyses conducted in this appendix, include the following: "The results of the analyses generally indicate that many of the biological measures evaluated exhibit a statistically significant adverse response to nutrient enrichment, however, the relationships between the biological response variables and nutrient levels were confounded by numerous other factors such as color, pH conductivity, and canopy cover. The confounding effects of these other variables result in weak statistical relationships between measures of the biological communities and nutrient levels. While FDEP believes the effect of nutrients on the biological communities is not clear enough to be used as the sole basis for establishing numeric nutrient criteria, the observed relationships between nutrients and the various biological measures demonstrate the need for nutrient criteria to prevent adverse biological effects in Florida streams." This conclusion seems questionable in light of the absence of an apparent effect between TP concentration and algal thickness and a weak affect at best between TP and chlorophyll a, and where inorganic nitrogen tended to be the only nutrient species with a positive association with increased aquatic plant growth. Even in the case of this nutrient species, whether the effect was a result of increased nitrate-nitrite or decreased stream color is unknown. The

11/19/2010 02:48 PM EST 2-4756Chapter 2 - Comment Documents Technical Support Document conclusions of Appendix B1 continue: "The statistical significance indicates that numeric nutrient criteria should be established and supports the decision to implement an alternative approach to deriving protective criteria, the Nutrient Benchmark Distribution Approach that is described in the Chapter 2f. While the analysis in this Appendix did not produce numeric thresholds that could be used as water quality criteria, the relationships that were determined, while relatively weak, do support the values derived using the Nutrient Benchmark Approach. Both the analysis of the RPS (regarding probability of increased algal thickness) and the analysis of the second change point in the stream periphyton response to nutrients indicate that the biological response to nutrient enrichment will generally occur at levels higher than the values generated using the Benchmark Distribution Approach." It is difficult to see how the results discussed in Appendix B1 or from the separate exploratory analysis presented earlier support the conclusion that "the relationships that were determined, while relatively weak, do support the values derived using the Nutrient Benchmark Approach." There appears, in fact, to be very little evidence from the RPS data presented that the proposed TP and TN criteria are related to aquatic plant attributes statewide. Where an association with a nutrient species is indicated, it is restricted to clearer flowing waters with lower canopy cover, and is not applicable to all waters represented in the dataset. Based on the analyses provided in Appendix B1 and supported by the algal thickness quartile analysis presented herein, it is clear that, for the purpose of developing effective nutrient criteria, not all nutrient species exhibit the same degree or even direction (positive or negative) of association with aquatic plant growth. Most specifically, evidence that TP concentrations have an impact relative to other nutrient species is limited to the discussion of a "co-limiting" effect in clearer, largely open streams. This would not seem to be sufficient basis for concluding that TP criteria established for all flowing waters of the state, whether divided by nutrient region or not, could be expected to provide a useful water quality management tool. The evaluations in Appendix B1 and provided here make very clear that careful consideration of individual nutrient species may be necessary to achieve scientifically defensible, useful numeric nutrient criteria. Generalizing certain associations to all nutrient species or to the total of all species such as TP and or TN should be avoided. In spite of the written conclusion in Appendix B1 that the available evidence supports the need for numeric nutrient criteria for TP and TN concentrations, the information presented in the appendix and in the exploratory data analysis presented here contradict that conclusion.
There is evidence that both color and percent canopy cover should be considered as factors influencing the potential for algal growth in flowing waters. Sources of color are typically natural, with patterns of annual variation that should be generally consistent from year to year. Therefore, "colored" flowing waters should largely remain as such, and this should be incorporated into numeric criteria as is being proposed for lakes. In addition, much of Florida is currently forested, and substantial deforestation along the banks of flowing waters is unwise from a water quality and ecological perspective and unlikely as a result of the implementation of best management practices intended to sustain the many environmental and water quality benefits associated with forests. The absence of these factors from the flowing waters criteria proposed by EPA is not supported by available information. Conclusion The average algal thickness quartile evaluation described herein, in which general patterns between average algal

11/19/2010 02:48 PM EST 2-4757Chapter 2 - Comment Documents Technical Support Document growth and a number of explanatory variables including TP and TN concentrations are described, provides little support for the view that EPA's proposed nutrient criteria for TP and TN in flowing waters will lead to improved water quality management or reflect levels of nutrients associated with attainment of DUs, at least with respect to algal growth. While percent canopy cover and stream color were relatively strongly associated with average algal thickness, associations with TP and TN concentrations were not apparent. In general, these findings are consistent with those described by FDEP in its analysis of the Rapid Periphyton Survey in Appendices B1and B11 of the EPA TSD. Other water qualityvariables also appear to be more strongly associated with average algal thickness, although the presence of a causeeffect relationship cannot be determined. These observations suggest that attainment of the proposed TP and TN criteria would do little to improve water quality in these flowing waters. This analysis also suggests that any numeric nutrient criteria development scheme for Florida flowing waters should explicitly incorporate stream color, canopy cover, and other light attenuating conditions beyond consideration of nutrient watershed regions. 

# Comment ID 1292-1.001.089
Author Name: Wiegand P. Organization: National Council for Air and Stream Improvement, Inc. Need to Evaluate Predictive Accuracy and Define Acceptable Uncertainty As noted by EPA and supported by the FDEP data analysis provided in Appendix B-1 (docket file EPA-HQ-OW-2009­ 0596-0003.16.pdf), which examined data for primary response variables such as chlorophyll a and periphyton thickness as well as SCI, there is little indication of cause-effect relationships between possible response variables and nutrient concentrations. In its preamble, EPA states: "EPA analyzed stressor-response relationships in Florida streams based on available data, but...did not find sufficient scientific support for their use in the derivation of numeric nutrient criteria for Florida streams. More specifically, EPA was not able to demonstrate a sufficiently strong correlation between the biological response indicators (e.g., chlorophyll a, periphyton biomass, or SCI) and TN or TP concentrations. Thus, the Agency could not confidently predict a specific biological response (such as an SCI score) for an individual stream solely from the associated stream measurements of TN or TP concentrations." Without specifically discussing the analyses in Appendix B-1 or providing its own analyses, EPA goes on to state that: "There may be several reasons why empirical relationships between field derived data of nutrient stressor and biological response variables show a relatively weak correlation." Two are mentioned in general terms. One is "other stressors" that EPA notes can confound or obscure relationships between nutrient and response variables. An example of "excessive scour" 68 is given, which EPA states "could cause low benthic invertebrate diversity, as measured by the SCI, even where nutrients are low." The second reason given: "is that algal biomass accumulation is difficult to characterize because dynamic conditions in an individual stream can allow algae to accumulate and be removed rapidly, which is difficult to capture with periodic monitoring programs."

11/19/2010 02:48 PM EST 2-4758Chapter 2 - Comment Documents Technical Support Document Both statements are true. However, the analysis of data by FDEP included in Appendix B1 represented a substantial effort to remove the effects of confounding variables and still determined that relationships were weak for some nutrient variables and nonexistent for others, including TP. In addition, the protocols for collecting SCI data specifically limit the potential for SCI to be influenced by unusually high or low flows (FDEP 2007). The second reason is related to the first in that flowing water systems are dynamic and values of causal and response variables change in ways that may not be captured by existing monitoring programs. EPA then presents its alternative basis for the proposed nutrient criteria, a reference/percentile approach using TN and TP concentrations "associated with a healthy biological condition in streams." It is important to note that "healthy biological condition" is determined using the same SCI data that EPA suggested in the previous paragraph could be affected by "excessive scour" (again, FDEP SCI protocols appear to limit the potential for SCI to be influenced by unusually high flows, although SCI can clearly be affected by factors other than nutrients). A reasonable alternative interpretation of the available data and analysis is that there is little evidence, in spite of a considerable amount of data and detailed analysis, to support the identification of numeric nutrient criteria that are predictive of designated use impairment. Consequently, EPA appears to be proposing criteria for Florida's flowing waters that reflect little more than a crude conceptual model that excess nutrients can negatively affect aquatic ecosystems. Such an approach is unlikely to yield numeric nutrient criteria that can be used to predict designated use impairments with much confidence and therefore should be of concern if implemented as a basis for managing the quality of Florida's flowing waters. Because criteria must be predictive and uncertainty will always be present, an evaluation of the ability of criteria to predict designated use impairment and to account for uncertainty where possible is necessary. A section of the empirical approaches guidance is devoted to a discussion of these related topics. The SAB Committee affirmed their importance, and went further to call for incorporation of a systematic planning effort to develop a basis for judging how much uncertainty is acceptable. EPA has not conducted, or at least has not included in related technical development documents, any such planning effort. One of the most important ways to minimize uncertainty in the ability of a criterion to predict biological/ecological impairments is to incorporate a biological measure into the criteria framework. The SAB Committee draft report states: "We agree with the statement in the Florida Department of Environmental Protection's letter of September 4, 2009 (letter from Daryll Joyner, Florida Department of Environmental Protection to Thomas Armitage, Designated Federal Officer, EPA Science Advisory Board Staff Office) indicating that the "most scientifically defensible strategy 69 for managing nutrients within the range of uncertainty is to verify a biological response prior to taking a management action." This risk/performance-based approach to setting nutrient criteria is evident not only in Florida's program, but also in those developed by California and Maine (Florida Department of Environmental Protection, 2009; Maine Department of Department of Environmental Protection, 2009; McLaughlin and Sutula, 2007)." (page 6) Other comments elsewhere in this document evaluate the proposed criteria with respect to the potential for errors in identifying designated use impairments. Further, a process is described that may be used to develop acceptable limits on these decision errors using either the stressor-response or the reference/percentile approach.

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# Comment ID 1671-3.001.020
Author Name: Brooks J. Organization: Florida Department of Environmental Protection DEP supports either merging regions in this manner for purposes of deriving TN criteria or the development of TN criteria that empirically account for the percentage of wetlands in a watershed. Appendix B-6: Extrapolating Natural Background Nutrient Concentrations of the EPA technical support document presented an analysis of a potential multiple regression model to determine the relationship between nutrient concentrations and human land uses in the watershed. The table on the following page contains correlation coefficients between land uses in the drainage area and nutrient concentrations. The correlation coefficient between percent wetland area within a drainage area and total nitrogen and organic nitrogen were 0.329 and 0.439, respectively. However, there was also a relatively strong negative correlation coefficient between percent wetland are and inorganic nitrogen (-0.383). This indicates that wetlands are important sources of organic nitrogen to Florida streams and an important sink for inorganic nitrogen. The relationship between nitrogen and wetlands was much stronger than any other nitrogen source, likely because of their contribution of organic nitrogen. Wetlands represent a natural organic nitrogen source that should not be mitigated. It should be noted that upland forested areas have a much greater influence on both nitrogen and phosphorus concentrations than any other land use, but in the opposite direction (a sink vs. a source). This is also important to keep in mind later in the document in the discussion of the impacts (or lack thereof) of silviculture on concentrations of nutrients in streams. Original comment letter contains additional information in Table B8-1 Correlations Between Nutrient Variables and Percent Land-Use and LDI from Florida DEP proposed nutrient criteria comment report. See original comment letter. Original comment letter contains additional information in Table B8-4 Nutrient Variables vs Percent 2004 drainage areas land cover. LOESS regression lines and their confidence intervals were also plotted from Florida DEP proposed nutrient criteria comment report. See original comment letter. 

# Comment ID 1671-3.001.028
Author Name: Brooks J. Organization: Florida Department of Environmental Protection To evaluate the effectiveness of the LDI corridor approach, EPA's contractor, Tetra Tech, conducted an analysis to determine if landscape disturbance beyond the 100 meter buffer was associated with additional risk of nutrient enrichment. That analysis is contained in Appendix B-8 of EPA's Technical Support Document. That analysis supported the use of the 100 meter corridor approach in its conclusion that "For the 135 WBIDs evaluated, the near-field LDIs are a better predictor of TN and TP than the Stream Corridor LDI. However, the linear regression models developed, while statistically significant, provide little meaningful benefit (r2 < 10%) to using one of the alternative LDI approaches in

11/19/2010 02:48 PM EST 2-4760Chapter 2 - Comment Documents Technical Support Document comparison to the Stream Corridor LDI". Original comment contains additional information for streams and rivers in Figure 10. Stream Condition Index vs. Landscape Development Intensity Index. Within range of low LDI scores, there is no relationship between LDI and SCI. SCI shows significant decreases with LDI in higher LDI ranges (see DEP Nutrient TSD) from Florida DEP proposed nutrient criteria comment report. See original comment letter. Within range of low LDI scores, there is no relationship between LDI and SCI. SCI shows significant decreases with LDI in higher LDI ranges (see DEP Nutrient TSD). 

# Comment ID 1671-3.001.044
Author Name: Brooks J. Organization: Florida Department of Environmental Protection The findings concerning the lack of adverse effects of forestry operations on nutrient concentrations, as mentioned earlier by EPA in Appendix B-8 of their TSD (correlation matrix contained on page 15 of this document), corroborate FDEPs findings that forestry does not increase nutrient concentrations. It should be noted that forested areas have a much greater influence on both nitrogen and phosphorus concentrations than any other land use, but in the negative direction (a sink versus a source). The existence of a forest land use is expected to reduce nutrient concentrations.



# Comment ID 1671-3.001.045
Author Name: Brooks J. Organization: Florida Department of Environmental Protection 4. Comments on EPA's Concerns about 303(d) Listings for Benchmark Sites EPA asserted in Appendix B-9 of their TSD that some of DEP's nutrient benchmark sites should be excluded because they were listed as impaired waterbodies on a dated 303(d) list for Florida. However, much of the information EPA relied on was based on the 1998 303(d) list approved by EPA, which included many listings that were not based in reliable scientific evaluation and data. Furthermore, the primary criteria that were the basis for the listings at many of the reference sites were for dissolved oxygen (DO), coliform bacteria, and mercury. As described below, exceedances of these parameters should not automatically disqualify a site from being characterized as achieving a reference condition. It should also be noted that EPA considers many of these same sites to be EPA reference sites because they pass the SCI. 

# Comment ID 1671-3.001.075
Author Name: Brooks J. Organization: Florida Department of Environmental Protection

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1. Selecting a percentile for Total Nitrogen As stated earlier, Appendix B-6: Extrapolating Natural Background Nutrient Concentrations of the EPA technical support document presented an analysis of a potential multiple regression model to determine the relationship between nutrient concentrations and human land uses in the watershed. The analysis contained correlation coefficients between land uses in the drainage area and nutrient concentrations. The correlation coefficient between percent wetland area within a drainage area and total nitrogen and organic nitrogen were 0.329 and 0.439, respectively. The relationship between nitrogen and wetlands was much stronger than any other nitrogen source, likely because of their contribution of organic nitrogen. This indicates that wetlands are important natural sources of organic nitrogen to Florida streams and an important sink for inorganic nitrogen. If a nutrient criterion does not account for natural sources of nitrogen, large Type I errors are likely to occur. Therefore, DEP retrieved color, nitrogen and drainage basin land use data for DEP's reference (benchmark) stream stations to investigate the effect of natural conditions on achievement of EPA's proposed Downstream Protection Values (DPVs) for estuaries. Geometric means for organic nitrogen and color were calculated for each reference site (n=89). Additionally, the proportion of the drainage area covered by wetlands was tabulated, based on 2004 land use GIS coverages. Organic nitrogen was highly correlated with both percent wetland (spearman r=0.513) and color (spearman r=0.749; Figure 25). These results validate DEP's previous experience concerning the influence of natural processes and sources on nitrogen. Natural vegetation, which contributes large quantities of leaf litter and which is subsequently decomposed in wetlands, ultimately provides the source of both the color (humic acid substances) and organic nitrogen. The only anthropogenic sources of color in Florida waters are pulp and paper mills. As these are permitted discharges, DEP is fully aware that there are only four pulp mills discharging to Florida's freshwater streams. Furthermore, none of DEP's reference sites were downstream of Florida pulp and paper discharges. Therefore, the strong relationship between color and organic nitrogen is truly indicative of natural nitrogen sources. The influence of these natural processes on the attainment of the EPA proposed DPVs was investigated using both ordinary least squares regression and logistic regression. The difference between measured geometric mean organic nitrogen and the applicable DPV was calculated for each reference site. Organic nitrogen at sites with differences less than zero would attain the DPV, while those greater than zero would exceed the DPV. The relationship between these "difference values" and color is shown in Figure 26. Additionally, logistic regression was used to calculate the probability of organic nitrogen exceeding the DPV based on the influence of color alone (Table 4; Figure 26). The probability of exceeding the DPV increases dramatically as color increases. A second logistic regression model was constructed using both color and percent wetland area as independent valuables to predict organic nitrogen exceedance of the DPV (Figure 27). It should be noted that there is a moderate correlation between color and wetland area (r=0.413), reflecting the well known fact that wetlands act as a natural source of color, thus color and proportion of wetlands area are not completely independent variables. However, the logistic regression model including both color and proportion wetland area provided a better fit than did models with either variable alone. Furthermore, the addition of an interaction did not dramatically improve the fit or alter the relationship (Table 5) and is more difficult to visualize. Therefore, only the model based on color and wetland area is discussed further. The models illustrate the fact that as portion wetland area and/or color increase the probability of exceeding the DPV also increases. This same logic indicates that there is a high probability that minimally disturbed, wetland influenced sites would exceed In-stream Protection Values if the IPV did not account for natural sources of nitrogen.

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The strength of these regression models is quite remarkable considering the fact that they do not take into account the influence of the SPARROW calculated fraction delivered on the DPVs. Fraction delivered is essentially a function of travel time and distance from the terminal node and is independent of both color and wetland area, while the DPV is a function of a selected protective load to an estuary and fraction delivered. Wetlands will attenuate flow and lengthen travel time. However, the SPARROW model did not include wetland area as a variable. Additionally, the fraction delivered did not correlate with wetland area (r=0.082) and the relationship between wetlands and DPV exceedance is inverse to that which would be expected if the primary influence of wetlands on the DPV was to attenuate flow. The relationships between organic nitrogen and color and wetlands area represent natural processes. The degree to which large positive differences between measured organic nitrogen and the DPV (or high exceedance probabilities (>25%)) relate to natural conditions such as color or wetlands provides a clear indication that EPA's DPVs are gross underestimates of natural nitrogen level in Florida's streams. This also informs the decision on how to select an appropriate percentile given the high likelihood that organic nitrogen makes up the majority of total nitrogen in streams. DEP believes serious consideration needs to be given to establishing stream criteria for inorganic nitrogen (which is largely the result of anthropogenic activities) only because a large portion of the organic fraction in Florida streams is derived from natural sources. Alternatively, total nitrogen criteria should be adjusted to account for the influence of color and/or wetlands. Original comment letter contains additional information for streams and rivers in Table 3. Logistic regression models of probability of organic nitrogen in Florida reference streams exceeding DPV impairment as a function of color. McFadden's rho-squared (SYSTAT Software, Inc., 2004) is conceptually similar to the r-squared of linear regression. McFadden's rho-squared approaching 1.0 corresponds with more significant results. McFadden's rho-squared tends to be smaller than r-squared, so a small number does not necessarily imply a poor fit. Values between 0.20 and 0.40 indicate good results (SYSTAT Software, Inc., 2004) from Florida DEP proposed nutrient criteria comment report. See original comment letter. Original comment letter contain additional information for rivers/streams in Table 4. Logistic regression models of probability of organic nitrogen in Florida reference streams exceeding DPV impairment as a function of color and proportion drainage area as wetland of the Florida DEP proposed nutrient criteria comment report. See original comment letter. Original comment letter contains additional information for rivers and streams in Table 5. Logistic regression models of probability of organic nitrogen in Florida reference streams exceeding DPV impairment as a function of color, proportion drainage area as wetland, and interaction term between color and wetland area of the Florida DEP proposed nutrient criteria comment report. See original comment letter. Original comment letter contains additional information for rivers and streams in Figure 25. Relationship between color and organic nitrogen concentration in Florida's reference (benchmark) streams. Note that color accounts for nearly 60% of the variability in organic nitrogen of the DEP proposed nutrient criteria comment report. See original comment letter. Original comment letter contains additional information about streams and rivers in Figure 26. Relationship between color and the difference between measured reference stream organic nitrogen and the DPV and the probability of

11/19/2010 02:48 PM EST 2-4763Chapter 2 - Comment Documents Technical Support Document exceeding the DPV. Difference values greater than 0.0 represent reference sites with organic nitrogen in excess of the DPV; that is, sites that would exceed the criterion. The exceedance probability was calculated using the logistic regression presented in Table 3 of the Florida DEP proposed nutrient criteria comment report. See original comment letter. Original comment letter contains additional information about streams and rivers in Figure 27. Relationship between the probability of organic nitrogen in Florida reference streams exceeding the DPVs and color and proportion wetland in the drainage basin. Isobars indication the probability of exceeding the appropriate DPV for a given combination of color and proportion wetland. Probabilities were calculated based on the logistic regression presented in Table 5. The data points (black circles) are the measured color and proportion drainage areas as wetland values of the Florida DEP proposed nutrient criteria comment report. See original comment letter. 

# Response Comment IDs: 1292-1.001.076, 1292-1.001.089, 1671-3.001.045, 1671-3.001.028, 1671-3.001.044 Response: EPA received many comments on this section. These comments were organized into general themes and response prepared. Several comments disagreed with whether reference sites were appropriately selected. These comments included the general perspective that the Stream Condition Index (SCI) reference site selection method was arbitrary and simplistic. EPA has considered this and other comments. EPA notes that the reference set of streams used to derive the final criteria in the rule are different than the set of streams used to derive the proposed criteria, except in the West Central Nutrient Watershed Region (NWR). Other than the West Central NWR, EPA used a modification of FDEP’s benchmark reference set of streams, as described more fully in the final preamble and final TSD. For the West Central Region, EPA used the SCI reference stream set because there were insufficient benchmark sites within the West Central to calculate a percentile with confidence. As to the SCI reference site selection method, simplicity in and of itself is not generally an argument against a reference site selection method. The development of the SCI, used as the principal screening tool for the “biologically healthy” reference population, was not a simple process. The SCI incorporates a multitude of information in it, including rules for selecting least disturbed reference sites that were used to develop, score, and identify nutrient thresholds. Moreover, EPA disagrees that the method of selecting reference sites based on an SCI screen was arbitrary. EPA detailed in the TSD the lengthy, involved, scientifically defensible, and transparent process used to generate the multimetric index; a process that is based on well established EPA guidance and scientific principles. The bioassessment and bioindicator literature underlying the SCI is both broad and comprehensive. Similarly, the selection of an SCI threshold of 40 was not arbitrary, but rather based on two rigorous statistical analyses detailed in the TSD. EPA considered a variety of potential SCI endpoints, as detailed in the TSD, and concluded that a value of 40 was most defensible. EPA wanted to develop a reference selection process that was both defensible and clear. The process EPA proposed depended on easily replicable bioassessment results that are clear to identify and easy to use in selecting sites. The SCI also clearly responds to stressors, including nutrient stressors, as detailed in the TSD and citations therein. Other comments opposed the use of the SCI alone for site selection, arguing that natural conditions can influence the SCI tool performance including physical-chemical parameters such as velocity, conductivity, pH, temp, and DO which can act as natural stressors. Natural variability does influence SCI scores, as reflected in the variability around minimally impacted reference sites SCI scores. EPA considered the influence of this natural variability explicitly in the selection of the SCI threshold and this consideration is described in great detail in the TSD appendices B-13 and B-14. There is also a great deal of information about

11/19/2010 02:48 PM EST 2-4764Chapter 2 - Comment Documents Technical Support Document human disturbance incorporated into the SCI score. For example, the development of the SCI included responsiveness to human disturbance gradients, including the Land Disturbance Index (LDI), in the selection, scoring, and threshold selection processes. So, the SCI scores inherently include considerations of human disturbance, and the selection of the threshold incorporates considerations of least-disturbed conditions. Lastly, the SCI was not used alone for reference site selection. CWA section 303(d) listing information was also used in screening sites for inclusion as reference sites. Other comments disagreed with the use of low dissolved oxygen as a basis to reject candidate reference sites because low oxygen may be a natural occurrence. EPA considered this and other comments. EPA retained the removal of sites listed by FDEP as impaired for dissolved oxygen for both the modified benchmark and SCI reference populations as detailed in the final rule and TSD. EPA rejected sites because of low dissolved oxygen where those sites had been included by FDEP on Florida’s list of impaired waters, pursuant to section 303(d) of the CWA. FDEP is not required to include waterbodies on the section 303(d) list where it demonstrates that concentrations of dissolved oxygen were measured below the numeric criteria due solely to natural conditions. Without such a demonstration, EPA must rely on FDEP’s identification of impairment when considering whether to select candidate reference sites. Concerns related to FDEP’s section 303(d) list should be addressed through the 303(d) listing process, which is independent of the nutrient criteria development process. Similarly, any comments about the appropriateness of Florida’s dissolved oxygen criteria should be addressed in FDEP’s criterion development process and not the nutrient criteria process. Some comments objected to the rejection of WBIDs listed as impaired for mercury or coliforms. EPA did not exclude WBIDs that were listed as impaired for any constituent other than dissolved oxygen and nutrients. This is detailed in the draft and final rule and TSD. Lastly, with regards to reference site selection, some comments sought clarification on the SCI reference approach. EPA provided a lengthy and clear description of the straightforward process used for selecting the SCI Population reference sites, which included a detailed description of the development of the SCI itself, in section 2 of the proposed rule TSD. There is a well established, sizeable body of scientific knowledge including both experimental and observational studies, including in Florida, that has unequivocally established a cause and effect relationship between nutrients and biological responses in fresh water lotic ecosystems, including an effect on the balance of natural aquatic flora and fauna (e.g., Elwood et al. 1981, Bothwell 1985, Peterson et al. 1985, Moss et al. 1989, Dodds and Gudder 1992, Rosemond et al. 1993, Bowling and Baker 1996, Bourassa and Cattaneo 1998, Biggs 2000, Francoeur 2001, Rosemond et al. 2001, Rosemond et al. 2002, Notestein et al. 2003, Slavik et al. 2004, Gaiser et al. 2005, Cross et al. 2006, Mulholland and Webster 2010 and see final rule and final rule TSD). EPA has concluded from this body of scientific knowledge that a cause and effect relationship between nutrient enrichment and detrimental biological responses exists and that nutrient reduction will result in environmental improvement. EPA received related but distinct comments that stressor-response relationships were insufficient to derive nutrient criteria in Florida. EPA considered a range of stressor-response analyses for deriving nutrient criteria in Florida and concluded that there was a lack of the necessary combination of data regarding potentially confounding factors that influence the empirically estimated relationship between nutrients and response variables to support the use of the stressor-response methodology in this context. Therefore, for the final rule, EPA utilized the reference condition approach to derive numeric criteria for Florida streams as described in previously published and peer-reviewed national nutrient criteria guidance. A number of comments disagreed with the sufficiency of data used by EPA. EPA considered these and other comments. The first assertion was that EPA used limited data. EPA considered all available data of defensible quality. For both the proposed and final

11/19/2010 02:48 PM EST 2-4765Chapter 2 - Comment Documents Technical Support Document rule for streams, this included screening and evaluating water chemistry data from more than 11,000 samples from over 6,000 sites statewide, and evaluating biological data of more than 2,000 samples from over 1,100 streams. A review of these data is included in the TSD and data files were also made available to the public. A second assertion was that data were collected during a fewclimatically abnormal years. It is unclear what is meant by climatically abnormal as Florida is typified by highly variable interannual climatic conditions (see figure below with annual precipitation data). Biological data were collected from 2004 to 2008, a period which, according to precipitation data from the Florida Climate Center, included years with annual average precipitationabove the 75th percentile of long-term average annual precipitation, years with annual averages below the 25th percentile of longterm average annual precipitation, and years with annual averages equal to the long-term average annual precipitation. Chemistry data were collected during an even longer period encompassing a similarly balanced number of variable climatic conditions. EPA concludes from this that the data used to derive numeric nutrient criteria incorporate the full range of hydrologic conditions representative of the variability typically observed in Florida including high, low and average conditions and that the range of conditions represented by the data actually reinforces the defensibility of the resultant criteria. Lastly, there were comments that weighting or averaging was needed when using data from multiple STORET stations within the same WBID. In response to this and similar comments, EPA considered the autocorrelation issues involved in using site averages for sites located closely in space and explored the use of WBID averages. For the final rule, EPA has decided to use WBID averages instead of site averages, which reduces the effect of spatial autocorrelation. The reanalysis and justification are detailed in the final rule and final rule TSD. The supplemental notice included analyses of WBID based spatial units. EPA received several comments that disagreed with the criteria determination process using the reference condition approach. EPA has considered these and other comments. For the final rule, other than the West Central NWR, EPA used a modification of FDEP’s Benchmark Reference Approach, as described more fully in the final preamble and final TSD. For the West Central Region, EPA used the SCI reference stream approach because there were insufficient benchmark sites within the West Central to calculate a percentile with confidence. The first comment within this general topic was that use of the upper bound of the distribution for “healthy” streams compromises the criteria. EPA considered several options for percentiles and incorporated the concern reflected in this comment into its consideration of which percentiles to use in the final rule. For the final rule, other than the West Central Region, EPA is using the 90th percentile of the modified Benchmark Approach WBID averages within each region because of EPA’s confidence in the screening of that reference population. In the West Central, EPA is using the 75th percentile of SCI approach WBID averages because of reduced confidence in the quality of sites within that population and the reduced sample size. The details of this decision and analysis are included in the final rule and final rule TSD. EPA concluded that a reference population typified by either healthy biological conditions or least-disturbed conditions provides EPA with the confidence that these are least-disturbed sites and that the use of upper bound percentiles from this population to establish the criteria was acceptable. A second related comment was that no analysis had been provided to support the 75th percentile as an accurate statistic for defining the distribution of reference sites and that its selection was a policy and not technical decision. As stated above, in response to this and similar comments, EPA revisited the percentile selection process and decided on the percentiles indicated above. EPA defends the selection of an upper percentile of biologically healthy and least disturbed populations of values as technically defensible for protecting streams. Again, EPA provided a detailed argument of why that is so, related to the fact that the nutrient dynamics of such sites are, implicitly, consistent with that found in sites supporting designated uses. EPA also affirms that the 75th percentile is indeed a statistical characteristic of a population distribution. EPA agrees that the final decision to use a specific percentile does include the exercise of judgment, but that judgment is not arbitrary but rather is based on a consideration of risk to uses based on the degree to which the basis population represents conditions expected to support uses and a consideration of errors in making use attainment decisions based on the resultant values. This judgment is informed by technical information as well.

11/19/2010 02:48 PM EST 2-4766Chapter 2 - Comment Documents Technical Support Document Lastly, some comments asked why a 90th percentile was not used, as suggested by FDEP. Again, EPA has finalized streams criteria for most regions using the 90th percentile when there are sufficient data available to provide EPA with enough confidence that the reference site population is least-disturbed, and closely reflective of minimally impacted conditions. In the West Central Region, where fewer reference sites are available, EPA has continued to set the criteria at the 75th percentile because there is less confidence that these sites reflect least-disturbed conditions. In the absence of a clear, un-confounded stressor-response relationship, EPA elected to use a reference condition approach to develop protective numeric criteria. For the proposed criteria and for the final rule criteria in the West Central, from the distribution of sites with documented healthy biological communities (i.e., SCI >= 40), filtered to remove nutrient and nutrient related (e.g., DO) impairments, EPA chose the nutrient levels associated with the 75th percentile. EPA selected the 75th percentile for the SCI based population consistent with recommended national guidance to provide a reasonable consideration if inherent uncertainty in condition associated with a biologically healthy population only. EPA was not confident that nutrient levels associated with a higher percentile, e.g., the 90th percentile, would be sufficiently protective of aquatic life in the West Central, based on the SCI population given the inherent uncertainties in the process, and EPA’s statutory and regulatory responsibility to promulgate water quality criteria that are fully protective of the designated use. Again, as noted above for regions other than the West Central, for the final rule, EPA has relied on a more stringent process for selecting least-disturbed sites that allow the use of a higher percentile, because there is less uncertainty in the consistency of that population with protection of designated uses. For those regions, EPA has selected the 90th percentile of its modified benchmark population of reference sites.

Comment IDs: 1671-3.001.020, 1671-3.001.075 Response: EPA received comments disagreeing with how the Agency decided to classify streams into Nutrient Watershed Regions (NWRs). EPA has considered these and other comments. For the final rule, EPA has decided to split the Panhandle region into West and East regions and to restrict the size of the West Central (previously Bone Valley) region. There were several comments related to intraregional classification. The first comment was that the approach for regionalization was too broad, that criteria will not protect the diversity and unique characteristics of waters that vary within regions, and that site-specific studies and criteria would account for more variability. As outlined in the nutrient criteria guidance, EPA recognizes that classification aims to reduce as much natural variability within classes as possible. Such classification efforts must weigh the trade-off between specificity, which would be optimized if each site were considered separately, and resource requirements and data availability, which clearly limit how fine a classification is possible. EPA considered a variety of regionalization schemes and has decided on the regionalization described above and detailed in the final rule and final rule TSD. EPA believes the regionalization is protective of Florida streams since EPA considered the full range of variability in its selection of sites and captures that variability in its selection of the SCI thresholds based on inter-site variability among reference sites and in its selection of the upper bound percentiles of the reference population.
A second comment related to stream classification was that 4th order streams are different from 1st order streams in structure and function and in responses to nutrient loads. EPA agrees that size can affect stream processes and EPA considered stream size, but did not find a compelling basis for differentiating criteria based on stream size for the final rule since stronger differences were attributable to interregional classes as detailed in the proposed rule and final rule TSDs. EPA would not rule out regional refinement in the future based on stream size should compelling evidence support such a change. The federal site-specific

11/19/2010 02:48 PM EST 2-4767Chapter 2 - Comment Documents Technical Support Document alternative criteria procedure established in the rule may be used for such changes when additional scientific consideration can bring added precision or accuracy to express the necessary level or concentration of a water quality parameter that is protective of the designated use. A third comment is that stream classifications should have been based on concentrations and not N:P ratios. EPA agrees that N:P ratios along should not be the sole basis for classification which is why EPA considered concentrations as well as N:P ratios in its classification and detailed this in the draft rule and final rule TSDs. There were also several comments related to interregional classification elements. Some comments argued that soil and geologic differences were related to P but not N and, therefore, were not appropriate bases for NWR for nitrogen. EPA considered many factors related to classification and considered several classification options. Clearly, there are differences among the regions with respect to geologically reactive P deposits, especially highlighted in differences between the North Central and West Central regions and other regions. EPA revisited the regionalization associated with the geologically reactive Hawthorn Group in response to these and other comments and selected the regionalization described above for both TP and TN, which is described in detail in the final rule and final rule TSD. EPA has chosen to use the same regionalization for TN criteria as it used for TP criteria. EPA recognizes that the original and revised regionalization relied heavily on underlying geological differences among regions that resulted in spatial differences in expected instream TP concentrations. Instream TN concentrations did not differ as strongly across these same regions as TP, and EPA received comments on the proposed rule that noted this difference and suggested that EPA consider alternative regionalizations for TN. EPA considered these comments and considered various options. For example, EPA observed that TN concentrations were associated with stream color, but EPA also noted that basing TN criteria on color assumes that changes in stream color are predominantly due to natural causes. Some variations in stream color, and associated changes in TN, are indeed due to natural variations in hydrology, geology, and vegetation, but in other cases these variations can be attributed to anthropogenic effects such as runoff or effluent. EPA could not sufficiently address these concerns with the data available at this time. As a result, EPA chose not to pursue a color-based TN criterion at this time. However, EPA would consider such an approach for site-specific criteria derivation where a color-TN relationship can be affirmed as being independent from anthropogenic influence. EPA also considered fewer stream Nutrient Watershed Regions for TN. EPA’s analysis of the stream TN data indicated that the two Panhandle NWRs, Panhandle East and West, exhibited TN concentrations lower than non-Panhandle NWRs (see final rule TSD), which led EPA to consider two NWRs instead of five. However, EPA’s statistical modeling indicated that a five NWR model explained no more or less variability than a two NWR model (see final rule TSD); this indicates that either approach is defensible. As a result, for consistency in application of criteria and in deference to the co-limiting nature of TN and TP, EPA has decided that similar regionalization for TN and TP is both defensible and protective of designated uses. Other comments suggested that geology was an appropriate basis for regionalization, but that biological comparisons should also be used to identify regional differences. EPA’s regionalization began with a framework developed by FDEP that was based on biology. The FDEP effort considered bioregions from their bioassessment programs as one element in their classification framework. Not surprisingly, the final EPA NWR classification is similar to the bio-regionalization developed by FDEP for their SCI tool, with some obvious differences dictated by geological factors. Lastly, EPA received comments that nutrient availability is controlled by soil chemistry, geology, and hydrogeology and that classes should be based on these factors for areas with adequate supporting data. EPA agrees and considered all of these factors, data availability, and appropriate response characteristics in establishing the NWR classes. Soil chemistry reflects underlying geology, which was an element used by EPA in developing the NWRs. Similarly, EPA considered ecoregions which themselves rely heavily on geology, soil type, and hydrology. Importantly, however, EPA also considered trends in observed nutrient distributions to verify and guide classification. It is the behavior of nutrients that manifests

11/19/2010 02:48 PM EST 2-4768Chapter 2 - Comment Documents Technical Support Document the effects of the major classification drivers, so EPA relied on this to help guide final class selection.

Comment ID: 1011.001.004 Response: EPA received comments critical of evenness in the derivation of criteria across regions. The first comments suggested that differences in criteria depending across regions were unfair and punished regions that have been doing a good job of protecting their waters. EPA considered these comments and disagrees. For the proposed and final rules, EPA’s regionalization analysis did not consider effort expended to protect waters in determining the NWRs. The regionalization process is meant to reduce natural variability associated with geographic features important in determining instream nutrient concentrations, such as geology, hydrology, and soil types. There are certainly associations between human density, activity and water quality. But these associations do not factor into the regional classifications. Other comments expressed concern that Panhandle criteria were 2-4 times less than natural area concentrations. EPA considered this concern diligently and this is why the agency carefully identified sites for use in the reference condition approach that reflected least-disturbed and biologically healthy conditions. EPA argues that to the extent that samples from truly natural areas are reflected in the reference population, resultant criteria should minimize the risk of identifying these as impaired. In response to this and similar comments, EPA reconsidered classification that parts of the Panhandle appeared to have elevated nutrient concentrations due to natural geological factors. Consequently, the final rule regionalization splits the Panhandle into West and East regions to better reflect the natural differences across that region and reduce the errors expressed in these comments. EPA also received comment that the same standard should be set for the entire State so those with lower criteria don’t have to pay additional costs of treatment. EPA reaffirms that the object of classification was to reduce natural variability associated with geographic features important in determining instream nutrient concentrations, such as geology, hydrology, and soil types. Moreover, under the Clean Water Act, EPA cannot consider economic factors in establishing criteria to protect designated uses, so the effective cost of treatment of polluted water was not considered in deriving the criteria. EPA also received comments about inconsistencies in NWR descriptions and maps. One comment was that the method for assigning streams to regions was not consistent between shapefiles for NWRs and the Appendix B-18 list of estuarine DPV watersheds. EPA notes that DPVs to protect estuaries are no longer being considered under this rule, but will consider these concerns in linking any future estuarine DPV calculations to the NWR stream coverages and will reconcile any disparities at that time. EPA also received comment that there were inconsistencies between text of the report and the TSD -- specifically with regards to the Peninsula and Palm Beach County. EPA delineated NWRs using WBID coverages that adhere to watershed boundaries and these watershed boundaries were the intended boundaries. EPA revisited the southern Peninsula boundaries in response to these and other comments and has attempted to reconcile these issues and to produce unified language across the final rule and final rule TSD documents.

Comment ID: 1671-3.001.075 Response: EPA received several comments related to the TN and TP criteria and their appropriateness for criteria setting. The first of these argued that TN and TP were not predictive of steam health or stream impairments attributable to excessive nutrients. EPA disagrees with this assertion. First, there was substantial evidence presented of the presence of nutrient related impairments in stream and river systems across the State to justify the linkage between TN and TP and stream impairments. Second, There is a

11/19/2010 02:48 PM EST 2-4769Chapter 2 - Comment Documents Technical Support Document well established, sizeable body of scientific knowledge including both experimental and observational studies that has unequivocally established a cause and effect relationship between nutrients and biological responses in streams, including an effect on the balance of natural aquatic flora and fauna (e.g., Elwood et al. 1981, Bothwell 1985, Peterson et al. 1985, Moss et al. 1989, Dodds and Gudder 1992, Rosemond et al. 1993, Bowling and Baker 1996, Bourassa and Cattaneo 1998, Biggs 2000, Francoeur 2001, Rosemond et al. 2001, Rosemond et al. 2002, Slavik et al. 2004, Cross et al. 2006, Mulholland and Webster 2010). EPA has concluded from this body of scientific knowledge that a cause and effect relationship between nutrient enrichment and detrimental biological responses exists and that nutrient reduction will result in environmental improvement. Third, EPA received related but distinct comments that stressor-response relationships were insufficient to derive nutrient criteria in Florida. EPA considered a range of stressor-response analyses for deriving nutrient criteria in Florida and concluded that there was a lack of the necessary combination of data regarding potentially confounding factors that influence the empirically estimated relationship between nutrients and response variables to support the use of the stressor-response methodology in this context. Therefore, for the final rule, EPA utilized the reference condition approach to derive numeric criteria for Florida streams as described in previously published and peer-reviewed national nutrient criteria guidance. A second comment argued that it may be more appropriate to use alternative approaches to address increased biomass in streams, such as restoring retention time or limiting light. EPA again disagrees and has continued to use a regional reference condition based approach for deriving the final criteria as detailed in the final rule and final rule TSD. First, the comment implies nutrients are not responsible for excess algal growth, which is not accurate. As noted in several other responses and detailed in the proposed and final rule and proposed and final rule TSD, there is ample scientific evidence that nutrient enrichment contributes to excess algal growth and other stream ecosystem impacts. Second, riparian and stream restoration that restore retention time and lower light levels, where natural, might reduce some excess algal biomass but would more importantly improve overall stream quality independent of nutrient effects. However, this restoration will have only limited effect on reducing nutrient pollution in streams, merely passing the effects on to downstream ecosystems, which EPA is also required to protect. Lastly, while algae are certainly an important avenue through which nutrients impact streams, they are not the only avenue. Microbes, such as bacteria and fungi, also increase their productivity in response to nutrient enrichment and this detrital enrichment can also alter stream ecosystems (Cross et al. 2006, Rosemond et al. 2001, Rosemond et al. 2002). Increasing retention time and woody inputs would provide a milieu to manifest the effects of microbial enrichment from excess nutrients on stream ecosystem condition. A third comment was that TN criteria should be adjusted for color and wetland presence. This comment was based on evidence presented of the relationship between percent wetland, color, and TN concentrations, more specifically organic N concentrations which can dominate the TN pool in some regions. This relationship would imply an effect of natural organic N sources on TN dynamics that could be controlled through classification using color. EPA has chosen to use the same regionalization for TN criteria as it used for TP criteria. EPA recognizes that the original and revised regionalization relied heavily on underlying geological differences among regions that resulted in spatial differences in expected instream TP concentrations. Instream TN concentrations did not differ as strongly across these same regions as TP, and EPA received comments on the proposed rule that noted this difference and suggested that EPA consider alternative regionalizations for TN. EPA considered these comments and considered various options. For example, EPA observed that TN concentrations were associated with stream color, but EPA also noted that basing TN criteria on color assumes that changes in stream color are predominantly due to natural causes. Some variations in stream color, and associated changes in TN, are indeed due to natural variations in hydrology, geology, and vegetation, but in other cases these variations can be attributed to anthropogenic effects such as runoff or effluent. EPA could not sufficiently address these concerns with the data available at this time. As a result, EPA chose not to pursue a color-based TN criterion at this

11/19/2010 02:48 PM EST 2-4770Chapter 2 - Comment Documents Technical Support Document time. However, EPA would consider such an approach for site-specific criteria derivation where a color-TN relationship can be affirmed as being independent from anthropogenic influence. EPA also considered fewer stream Nutrient Watershed Regions for TN. EPA also considered fewer stream Nutrient Watershed Regions for TN. EPA’s analysis of the stream TN data indicated that the two Panhandle NWRs, Panhandle East and West, exhibited TN concentrations lower than non-Panhandle NWRs (see final rule TSD), which led EPA to consider two NWRs instead of five. However, EPA’s statistical modeling indicated that a five NWR model explained no more or less variability than a two NWR model (see final rule TSD); this indicates that either approach is defensible. As a result, for consistency in application of criteria and in deference to the co-limiting nature of TN and TP, EPA has decided that similar regionalization for TN and TP is both defensible and protective of designated uses. A fourth comment in this general theme was that the criteria established for TN and TP are overprotective because the criteria assume all forms of N and P contribute to water quality impairments in streams. EPA has a national policy of setting nutrient criteria for TN and TP. The basis for this policy is documented in the national nutrient criteria guidance documents. The last set of comments in this theme argues there are no documented benefits of TN reduction beyond that obtained through TP reduction. EPA disagrees. There is ample evidence in the literature that TP and TN both limit productivity in stream systems (Elser et al. 1990, Lohman et al. 1991, Francoeur 2001, Stelzer and Lamberti 2001, Elser et al. 2007). Reductions in both TN and TP are necessary, therefore, to control effects of excess productivity. Moreover, in streams naturally elevated by reactive P geology in Florida, which are concentrated in certain regions but present in places along the length of Florida, N limitation is most likely present and N reductions in such systems would reduce nutrient impacts. For this reason, EPA is finalizing both TP and TN criteria.

Comment IDs: 1292-1.001.051, 1292-1.001.074 Response: Requires no response.

References: Biggs, B.J.F. 2000. Eutrophication of streams and rivers: dissolved nutrient-chlorophyll relationships for benthic algae. Journal of the North American Benthological Society 19:17-31. Bothwell, M.L. 1985. Phosphorus limitation of lotic periphyton growth rates: an intersite comparison using continuous-flow troughs (Thompson River system, British Columbia). Limnology and Oceanography 30:527-542. Bourassa, N., and A. Cattaneo. 1998. Control of periphyton biomass in Laurentian streams (Quebec). Journal of the North American Benthological Society 17:420-429. Bowling, L.C., and P.D. Baker. 1996. Major cyanobacterial bloom in the Barwon-Darling River, Australia, in 1991, and underlying limnological conditions. Marine and Freshwater Research 47: 643-657.

11/19/2010 02:48 PM EST 2-4771Chapter 2 - Comment Documents Technical Support Document Cross, W.F., J.B. Wallace, A. D. Rosemond, and S. L. Eggert. 2006. Whole-system nutrient enrichment increases secondary production in a detritus-based ecosystem. Ecology 87: 1556-1565. Dodds, W.K., and D.A. Gudder. 1992. The ecology of Cladophora. Journal of Phycology 28:415-427. Elwood, J.W., J.D. Newbold, A.F. Trimble, and R.W. Stark. 1981. The limiting role of phosphorus in a woodland stream ecosystem: effects of P enrichment on leaf decomposition and primary producers. Ecology 62:146-158. Elser, J.J., E.R. Marzolf, and C.R. Goldman. 1990. Phosphorus and nitrogen limitation of phytoplankton growth in the freshwaters of North America: a review and critique of experimental enrichments. Canadian Journal of Fisheries and Aquatic Sciences 47: 1468-1477. Elser, J.J., M.E.S. Bracken, E.E. Cleland, D.S. Gruner, W.S. Harpole, H. Hillebrand, J.T. Ngai, E.W. Seabloom, J.B. Shurin, and J.E. Smith. 2007. Global analysis of nitrogen and phosphorus limitation of primary production in freshwater, marine, and terrestrial ecosystems. Ecology Letters 10: 1135-1142. Francoeur, S.N. 2001. Meta-analysis of lotic nutrient amendment experiments: detecting and quantifying subtle responses. Journal of the North American Benthological Society 20: 358-368. Gaiser, E.E., J.C. Trexler, J.H. Richards, D.L. Childers, D. Lee, A.L. Edwards, L.J. Scinto, K. Jayachandran, G.B. Noe, and R.D. Jones, 2005. Cascading ecological effects of low-level phosphorus enrichment in the Florida Everglades. Journal of Environmental Quality 34:717-723.

- Lohman, K., J.R. Jones and C. Baysinger-Daniel. 1991. Experimental evidence for nitrogen limitation in northern Ozark stream. Journal of the North American Benthological Society 10:14-23. Moss, B., I. Hooker, H. Balls, and K. Manson. 1989. Phytoplankton distribution in a temperate floodplain lake and river system. I. Hydrology, nutrient sources and phytoplankton biomass. Journal of Plankton Research 11: 813-835. Mulholland, P.J. and J.R. Webster. 2010. Nutrient dynamics in streams and the role of J-NABS. Journal of the North American Benthological Society 29: 100-117. Notestein, S.K., T.K. Frazer, M.V. Hoyer, and D.E. Canfield, Jr. 2003. Nutrient limitation of periphyton in a spring- fed, coastal stream in Florida, USA. Journal of Aquatic Plant Management 41:57-60. Peterson, B.J., J.E. Hobbie, A.E. Hershey, M.A. Lock, T.E. Ford, J.R. Vestal, V.L. McKinley, M.A.J. Hullar, M.C. Miller, R.M. Ventullo, and G. S. Volk. 1985. Transformation of a tundra river from heterotrophy to autotrophy by addition of phosphorus. Science 229:1383-1386. Rosemond, A.D., P.J. Mulholland, and J.W. Elwood. 1993. Top-down and bottom-up control of stream periphyton: Effects of nutrients and herbivores. Ecology 74: 1264-1280.

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Rosemond, A.D., C.M. Pringle, A. Ramirez, and M.J. Paul. 2001. A test of top-down and bottom-up control in a detritus-based food web. Ecology 82: 2279-2293. Rosemond, A.D., C.M. Pringle, A. Ramirez, M.J. Paul, and J.L. Meyer. 2002. Landscape variation in phosphorus concentration and effects on detritus-based tropical streams. Limnology and Oceanography 47: 278-289. Slavik, K., B.J. Peterson, L.A. Deegan, W.B. Bowden, A.E. Hershey, J.E. Hobbie. 2004. Long-term responses of the Kuparuk River ecosystem to phosphorus fertilization. Ecology 85: 939-954. Stelzer, R.S. and G.A. Lamberti. 2001. Effects of N:P ratio and total nutrient concentration on stream periphyton community structure, biomass, and elemental composition. Limnology and Oceanography 46:356-367.

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