## WATER QU ALITY TARGET REFINEMENT PROJECT

Task 3 : Water Clarity Target Development

Interim Report 3

Prepared for:

Charlotte Harbor National Estuary Program

1926 Victoria Avenue Fort Myers, FL 33901

- 3414

Prepared By:
Janicki Environmental, Inc.

1155 Eden Isle Drive NE. St. Petersburg, Florida 33704

February, 20 10

### 1.0 INTRODUCTION:

................................ ................................ .............. 1

1.1 Purpose

................................ ................................ ........................... 1

1.2 Location

................................ ................................ ........................... 1

1.3 Background

................................ ................................ ..................... 1

1.4 Objective

................................ ................................ ......................... 5

2.0 METHODS

................................ ................................ ......................... 5

2.1 Target Exceedances

................................ ................................ ........ 6

2.2 Observed vs Predicted K d



### ................................ ................................ 7

2.3 Tuning the Model Fit

................................ ................................ ........ 8

3.0 RESULTS

................................ ................................ .......................... 8

3.1 Target Exceedances

................................ ................................ ........ 9

3.2 Predicted vs Observed K d



### ................................ ................................ 11

3.2.1 Graphical Comparison

................................ ............................. 11

3.2.2 Residual Analysis

................................ ................................ ..... 16

3.3 Model Tuning

................................ ................................ ................. 19

4.0 DISCUSSION

................................ ................................ .................. 21

5.0 MANAGEMENT RECOMMENDATI ONS

................................ ......... 23

5.1 Target Identification:

................................ ................................ ..... 25

5.2 Assessment:

................................ ................................ .................. 301 

## 1.0 INTRODUCTION :

1.1 Purpose

The Char lotte Harbor National Estuary Program (CHNEP) is in the process of developing criteria to evaluate management actions using the extent of seagrass in estuarine waters as one indicator of estuarine health. These seagrass protection and restoration “targets” are being developed to meet objectives set forth in the CHNEP Comprehensive Conservation and Management Plan (CCMP). This project helps implement the following CCMP Quantifiable Objectives

**•** FW

- 1: Native submerged aquatic vegetation should be maintained and restored to a total extent and quality no less than caused by natural variation

, and

**•** WQ

- 2: Develop and meet site

- specific alternative criteria that are protective of living resources for dissolved oxygen, chlorophyll a , turbidity

, total suspended

so lids, salinity and pesticides.

Therefore, the targets represent management level indicators to track seagrass extent through time to evaluate the effectiveness of management actions in the watershed to minimize watershed impacts on estuarine seagrasses. Seagrasses are known to be primarily limited by the quantity and quality of light available for photosynthesis ; therefore, water clarity targets are needed to monitor a significant factor in determining the health and productivity of seagrass in Charlotte Harbor and associated estuarine

waters.

1.2 Location

The Charlotte Harbor Estuarine system is located in southwest Florida (Figure 1 ) and includes 224,000 acres (350 square miles) of estuaries downstream from a 3,008,000 acre (4,700 square mile) wate rshed. The CHNEP is a partnership of citizens, elected officials, resource managers and commercial and recreational resource users working to improve the water quality and ecological integrity of the greater Charlotte Harbor Watershed. A cooperative deci sion

- making process is used within the program to address diverse resource management concerns in the study area.

1.3 Background

A cornerstone of any effective resource monitoring program is the development, selection, and use of ecological indicators a ppropriate for the spatial and temporal scales defined for the assessment (Smith et al., 2006). The Charlotte Harbor National Estuary Program ( CH NEP) has developed a resourced

- based approach to derive water quality targets. The goal of the approach wa s t o achieve a water clarity that will allow
seagrasses to grow to their maximum observed depth (CHNEP 2006; Corbett and Hale 2006)

. The CH NEP has specified a minimum of 25% of the subsurface light reaching2 the maximum depth at which seagrasses occur in the greater Charlotte Harbor region based upon annual fixed seagrass transect monitoring and biennial aerial mapping throughout the region. The seagrass depth targets are then segment

- specific, based on a segmentation scheme developed for the Coastal Charlotte Ha rbor Monitoring Network (CCHMN : Figure 2 ); an inter

- agency monitoring network that samples water quality using a stratified, probabilistic sampling design (CHNEP 2006; Corbett and Hale 2006).

Figure 1 . Map of the Charlotte Harbor National Estuary P rogram study area.3 Figure 2 . Segmentation scheme used by the Coastal Charlotte Harbor Water Quality

Monitoring Network

.

Water quality and light availability are linked through a locally

- derived optical model from McPherson and Miller (1994) that relat es the concentrations of colored dissolved organic material (CDOM) , turbidity and chlorophyll a to the light attenuation coefficient ( K d

) (see CHNEP 2006; Corbett and Hale 2006). The coefficient K d defines the exponential decay rate in downwelling irradia nce as a function of depth as established by the Lambert

- Beer law (Kirk 1994). The combination of depth targets and the requirement for a minimum of 25% subsurface irradiance at those depths, allows for the

calculation of the CHNEP segment specific target s for the diffuse light attenuation coefficient, K d which are provided for convenience in Table 1

.4 Table 1. Charlotte Harbor National Estuary Program s eagrass depth targets and

corresponding target light attenuation coefficients ( K d

) (adapted from Tabl e 4 in CHNEP 2006). Segment Seagrass Depth Target (meters) Kd (m - 1 )

Lemon Bay 2.0 0.7

Cape Haze 1.9 0.7

East Wall 1.4 1.0

West Wall 1.4 1.0
Tidal Myakka 0.9 1.6

Tidal Peace 1.0 1.4

Tidal Caloosahatchee 1.0 1.4

Bokeelia 2.4 0.6

Pine Island Soun d 2.2 0.6

Matlacha Pass 2.0 0.7
San Carlos Bay 2.2 0.6
Estero Bay 1.6 0.9

The use of the light attenuation coefficient for setting management related water quality targets has been popularized as a management tool for translating light requirements

in to water quality targets capable of supporting seagrass communities ( Gallegos and Kenworthy 1996 ; Dixon and Kirkpatrick 1999 ; Gallegos 2001; Steward et. al

. 2005;

Smith et. al. 2006 ). Several resource managers have found it use ful for restoration and
prot ection efforts to estimate K d using linear combinations of commonly collected water quality constituents ( e.g., Gallegos 2001; Biber et al. 2008 ). These efforts are supported by Lorenzen (1972) who partitioned absorption and scattering components of the wa ter

column into four parts: water, phytoplankton, dissolved matter and non

- chlorophyll suspended matter. However

, it is widely recognized that partitioning of light attenuation

into linear components is only an approximation because the distribution and a vailability of light is not a linear function of partial attenuation component concentrations (Kirk

19 94 ). It is therefore imperative that linear light attenuation models be validated using empirical data whenever possible to ensure the representativeness of the model in predicting the light attenuation coefficient K d

.

The study area for the CCHMN encompasses a wide range of water body types differentially affected by freshwater inputs , tidal passes, circulation and other factors.

While K d targets differ by segment, the equation used to predict K d does not: the same equation is used for all segments. Gordon (198 9 ) classified water bodies as either Case I, where optical properties are governed primarily by phytoplankton; or Case II waters where optical p roperties are primarily governed by C DOM (Gallegos 2001 ). While both Case I and Case II waters were found to obey the Lambert

– Beer law, linear equations predicting K d have been found to rely on different sets of coefficients at threshold K d values of 0.2 7m - 1 (Duarte et. al. 2007).5 1.4 Objective

The development of resource based water quality targets has been an important accomplishment for the CH NEP and an important step in developing objective

environmental assessment tools that are both accurate and u seful to managers and policy makers who must present complex information to the general public. The validity and reliability of resource based targets are critical to the long term success of those management programs that utilize them

. I mplementing a sta tistically robust water quality monitoring program that collects data on water quality constituents used in the optical model (i.e., the McPherson and Miller 1994 ) and also collect ing empirical estimates of light attenuation has allowed the CHNEP to test t he validity and reliability of

the optical model now that several years of empirical data have been collected

. In this study

, we assess the optical model performance by comparing model predictions to empirically collected light attenuation data

.



## 2.0 METHODS

C urrently, the CH NEP evaluation strategy for the light requirements of seagrass uses the water quality data collected by the CCHMN as inputs into the optical model to derive

K

d ; however, the CCHMN also measures K d empirically. The instrument used for

meas uring Photosynthetically A ctive R adiation (PAR) was a LI

- COR Quantum ®

consist ing of one sensor to measure irradiance above the waters surface and another to

measure irradiance at various depths through the water column starting just below the

waters surfac e and increasing at intervals of approximately 0.2m to a depth close to the

bottom. L ight data are not collected at depths shallower than 0 .75 meters. Very recently (i.e. since 2008), the program has switched to using two underwater sensors to avoid

the co nfounding effects of cloud cover.

The study area is div i ded by two water management district jurisdictions. The dividing line between the Southwest and South Florida Water Management District lies at approximately at the southern end on Boca Grande Pass at latitude 2 6.42.00. The South Florida Water Management Distric t requires the use of a spherical light sensor that measures light captured from any angle while the SWFWMD requires a 2π cosine sensor that only measures downwelling irradiance. Irrespective of these differences, t he

calculation of K d is then derived by defining a slope of the natural log

- transformed sub

surface irradiance values as a function of depth to obtain an average change in irradiance with change in depth. This method , based on the Lambert Beer law, was adapted from the equation for downward irra diance described by Kirk (1994).

K

d = [

- Ln(E d (z 1 )/E d (z 2 ))] / z 2 - z 1 (1)

Where: E d = d ownward irradiance at depth d and Z= depth below waters surface in

meters.6 The optical model predictions used by Corbett and Hale (2006) were based on the

McPherso n and Miller equation (1994) :

K

d = 0.014*C 2 + 0.062* C 3 + 0.049*C 4 + 0.30 (2)

where K d equals the light extinction coefficient, C 2 is water color in Pt

- Co units, C 3 is turbidity in NTU and C 4 is chlorophyll a in micrograms per liter. Given this equation, the

minimum K d value is 0.30 and the positive coefficients determine that as concentration of any constituent increases from zero, the K d value increases. Increasing K d values correspond to decreasing water clarity meaning less light is ava ilable to seagrasses at depth.

Since both empirical and model based estimates of K d were available

, this presented the opportunity to evaluate the McPherson and Miller (1994) model performance relative to the empirical data on light attenuation collecte d concurrently with the water quality

data

. The analysis was restricted to the model domain from McPherson and Miller’s (1994) optical model (i.e. K d values <= 3.0 m - 1 ) which corresponds to the range of targets developed by Corbett and Hale (2006)

. The d ata w ere further screened to eliminate data collected prior to 10am and after 2pm to reduce the influence of solar angle on the empirical K d estimate. Where possible the empirical K d data were further subset to eliminate data where there was a large degree of uncertainty in the slope estimate (r 2 <0.70). These steps were taken to obtain a set of data where the observed

K

d was thought to reflect the true condition with increased confidence. Once these data were refined, the associated water quality data were used in the optical model to produce a model

- based (predicted) K d value. The predicted and observed K d could then be compared to evaluate how well the optical model predicted the observed K d . The analysis assumed that the observed K d is without error and represents the “true” light

attenuation in the water column.

M odel performance was evaluated in three ways :

1. Modeled and empirical estimates of K d were compared in the context of percent exceedances of the target s derived by Corbett and Hale (2006)

. 2. D if ferences between modeled and empirical data were described across the range of K d values using statistics

. 3. Attempt s were made to improve model performance where modeled and empirical data d id not agree

.

2.1 Target Exceedances

To examine the difference in target exceedances, c ontingency tables (2X2) were constructed to examine the exceedance frequencies predicted by the model compared to exceedance frequencies calculated using the empirical K d data. McNemars test (Stokes et al. 2000) was used to assess agreement between measures of light attenuation. Since at each sampling location, water quality data were collected (used in7 the model predictions) and K d was also measured, the test statistic is constructed based

on the fact that the observations are mat ched (i.e., measured on the same experimental unit). The test statistic considers only those measurement s that were discordant with respect to predicting K d exceedances (i.e., the model predicts an exceedance when the observed data suggest a non

- exceedance or vice versa). The test statistic follows a chi square distribution and therefore a statistic for one degree of freedom greater than 3.841 (alpha=0.05) equates to a significant result.

2.2 Observed vs Predicted K d

To evaluate model predictions across the range of the K d targets within the study area, descriptive plots were generated comparing model predictions and observed values for each segment . Simple linear regression analysis was used to test agreement of modeled and empirical data by testing the nul l hypothesis that the intercept was not different from zero and that the slope was not different from 1. Reject of either null hypothesis suggests disagreement between the observed and modeled K d . The

difference between modeled and observed K d was also qua ntified using the prediction error (i.e. residuals)

. The residuals were calculated by subtracting the observed K d ( О )
from the predicted K d ( ˆ **φ** ).

Residual = 

# ˆ ( ) **φ φ**

**−**

If the model accurately reflected the observed condition then the expectation is that the

residuals would be centered on zero. Prediction b ias was calculated as the average difference between the predicted and observed K d

. Residuals were also plotted as a function of water quality constituents to examine if prediction bias was a function of constituents both inside and outside the model equation.

Bias =

The Mean Square Error (MSE) is a statistic that estimates the precision of the model in capturing the true K d value. Smaller MSE values correspond to increased precision indicating better reliability.

MSE = 2 2

error 

## Bias **σ +** 

Wher e:

σ 2

error = variance of the residuals

Since the magnitude of the light attenuation coefficient varied by segment, a coefficient of variation was calculated by dividing the square root of the MSE by the mean of the

observed K d to compare the disp ersion relative to the observed segment mean K d

. While no specific criteria were specified for determining acceptance or rejection of the model based on these statistics it was helpful to compare the values among segments

to determine their relative validi ty and reliability with respect to model predictions. (3)

(4)

(5) 

### ˆ ( )

N **φ φ**

**−** 

# ∑8 2.3 Tuning the Model Fit

A ttempts were also made to improve the model fit to the observed data in segments where model predictions and observed data did not agree. Segment specific regressions were attem pted using the optical model param e ters as well as total nitrogen (mg/ L ), total phosphorus (mg/ L ) and total suspended solids (mg/ L ). The segment specific regressions were applied using a stepwise regression that selects order of inclusion to the regression model based on the relative contribution to the overall R

square statistic and retains only variables that contribute to the model with statistical significance at alpha< 0.05 (SAS Institute Inc. 2006). Data were also aggregated monthly and segment speci fic regression equations derived of the monthly averages of the water quality constituents to examine the effects of a veraging data on model predictions.



## 3.0 RESULTS

The sample size and period of record for the water quality data used in this effort is

list ed by segment in Table 2

. Between 200 and 300 observations were analyzed in each
segment coinciding with a n approximate 7 year time period between 2002 and 200 8

. The table is divided into the upper and lower portions of the study area designated as Upper C harlotte Harbor and Lower Charlotte Harbor, respectively. Segment average

observed K d estimates ranged from 0.94 in Lemon Bay and East Wall to 2.44 in the

T idal Caloosahatchee River ( Table 3 )

. The segment average K d values translate to an

average depth at which 25% of the subsurface irradiance reached the bottom from 1.47

m and 0.47 m in Lemon Bay and Tidal Caloosahatchee, respectively. Observed
segment average water quality concentrations for optical model parameters as well as

other relevant potential attenuators of light in estuarine environments are also provided

in Table 3

.9 Table 2. Water quality data period of record and number of observations for each segment of the Coastal Charlotte Harbor Monitoring Network.

Segment Number of

O bservations Period of Record

Upper Charlotte Harbor Cape Haze 2 57 Oct 2002

– Jul 2008

East Wall 31 1 Oct 2002

– Jul 2008 Lemon Bay 27 9 Oct 2002

– Jun2008 Tidal Myakka 2 89 Oct2002

- Jul 2008

Tidal Peace 3 0 4 Oct2002

- Jul 2008

West Wall 32 1 Oct2002

- Ju l 2008

Lower Charlotte Harbor

Bokeelia 3 82 Apr2002

– Nov2008 Estero Bay 248 Sep 2003

- Jul 2008

Matlacha Pass 331 Mar2002

- Jul 2008

Pine Island Sound 23 4 Sep2003

- Jul 2008 San Carlos Bay 190 Mar2002

– Jul 2008

Tidal Caloosahatchee 2 29 May2002

- Jul 2008

Table 3. Grand averages for water quality parameters relevant to light attenuation collected by the Coastal Charlotte Harbor Monitoring Network by segment.

Segment K d (m

- 1) Color (PCU) Turbidity (NTU) Chla (μg/l) TP (mg/l) TN (mg/l) TOC (mg/l) TSS (mg/l) Upper Charlotte

Harbor Lemon Bay 0.94 13.34 4.18 5.13 0.13 0.58 5.05 22.67

East Wall 0.94 36.25 1.85 5.50 0.17 0.66 8.10 14.53 Cape Haze 1.01 25.98 2.87 6.09 0.14 0.68 6.50 22.13

West Wall 1.20 48.82 2.34 6.93 0.23 0.78 9.81 14.25 Tidal Myakka 2.04 84.33 4.07 8.76 0.26 1.01 14.21 13.40

Tidal Peace 2.07 79.67 4.35 10.45 0.41 1.08 13.86 12.68

Lower Charlotte

Harbor

Bokeelia 1.02 20.49 1.33 4.06 0.08 0.43 3.34 15.10 San Carlos Bay 1.07 13.00 1.76 9.57 0.05 0.45 5.53 14.88

Pine Island 1.21 14.23 2.14 4.85 0.04 0.55 5.24 16.11 Estero Bay 1.53 25.73 3.12 5.16 0.05 0.59 6.39 16.33

Matlacha Pass 1.91 22.42 1.35 5.35 0.07 0.47 8.84 15.23

Caloosahatchee 2.44 68.69 3.84 9.49 0.12 1.04 12.50 8.44

3.1 Target Exceedances

Both model predictions and observed K d frequently exceeded the K d targets established by Corbett and Hale (2006 )

. Overall exceedance frequencies ranged from 4 0 % to 82%10 for observed K d and 44% to 78% for model prediction s ( Table 4 ). During the wet season (i.e., July through November ) water quality was only sufficient ca. 25% of the time in any
segment

. I n Upper Charlotte Harbor, a significant difference in expected exceedance proportions between observed and predicted K d was found in Cape Haze, Tidal Peace and West Wall ( Table 5 ).

Table 4. Percent of the model predictions that exceeded targets values by segment and season. Segment Percent Target Exceeda nce Dry Wet Overall Upper Charlotte Harbor

East Wall 20 79 44 Cape Haze 71 88 78 Lower Lemon Bay 70 77 73 Tidal Myakka 44 72 53

Tidal Peace 49 81 60

West Wall 46 89 62

Lower Charlotte Harbor

Bokeelia 43 64 53 Estero Bay 35 73 51

Matlacha Pass 43 61 49

Pine Island Sound 62 90 74 San Carlos Bay 44 68 5 3

Tidal Caloosahatchee 51 75 6011 Table 5

. Light attenuation ( K d ) target exceedance percentages using the observed and modeled data. Analysis was limited to data where observed K d ) was less than 3. A ** indicates significant difference at alph a=0.05 based on McNemars test.

Upper Charlotte Harbor Percent Exceedance

Segment Observed Predicted

East Wall 40 44

Cape Haze ** 65 78

Lemon Bay 75 73

Tidal Myakka 47 53

Tidal Peace ** 49 60

West Wall ** 49 62

Lower Charlotte Harb or Percent Exceedance

Segment Observed Predicted

Bookelia** 75 53

Estero Bay** 75 51

Matlacha Pass** 82 49

Pine Island Sound 78 74

San Carlos Bay** 82 53

Tidal Caloosahatchee** 75 60

The model predicted a larger proportion of target exceedances than the observed K d data in these segments . These differences were principally driven by differences in the

wet season exceedance frequencies . In Lower Charlotte Harbor, Pine Island Sound was the only segment where observed and predicted exc eedance frequencies were not significantly different

. Under prediction of observed K d was prevalent with d ry season predictions principally responsible for differences between observed and modeled

exceed a nces in Lower Charlotte Harbor

.

3.2 Predicted vs O bserved K d

3.2.1 Graphical Comparison

A graphical comparison of the predicted vs observed K d is provided for Upper Charlotte Harbor segments ( Fig ure 2 ) and for Lower Charlotte Harbor segments ( Fig ure 3 ). The solid line in the plots represents a 1:1 rel ationship indicating the line of perfect agreement between predicted and observed values. The broken line is a regression line comparing the observed and predicted K d

. In all segments the regression analysis12 suggested a significant difference in both inte rcept (from zero) and slope estimate (different from 1) indicating that the prediction errors w ere dependent on where along

Figure 2

. Predicted vs observed K d plots for Upper Charlotte Harbor segments.13 Figure. 3 . Predicted vs observed K d plots for Lower Charlotte Harbor segments.14 the range of empirical K d the model value was estimated

. In all segments, lower values

of K d were over predicted by the model while higher values were under predicted. Especially noticeable was that many observed measurements were near or below

0.30m

- 1

, the minimum light attenuation predicted by the model . The frequency of values

below 0.30 ranged from 2% of the observations in San Carlos Bay to 11% of the

observations in East Wall

. The average of the segment minima observed K d value over the study period was 0.11m

- 1.

The average contribution of each parameter to the model predictions varied among segments and between seasons ( Figure 4 ). The highest percent contribu tion of the intercept to the total K d in the dry season was Pine Island, San Carlos Bay, Bokeelia and Lemon Bay. These segments tended to have the lowest percent contribution of color and the highest percent contribution of chlorophyll, especially in the wet season. Matlacha Pass had a relatively consistent contribution of color across seasons but increased influence of chlorophyll in the wet season.15 Figure. 4 . Percent contribution of optical model constituents to the total l ight attenuation in each segment in the dry season (Top) and wet season (bottom). Model constituents from bottom to top are: Intercept, Color (PCU), Turbidity (NTU), and Chlorophyll a (μg/l). 0% 20% 40% 60% 80% 100% Intercept Color Turbidity Chla

0% 20% 40% 60% 80% 100%

Bokeelia Cape Haze East Wall

Lower Lemon Bay Tidal Myakka Tidal Peace West Wall Caloosahatchee Estero Bay Matlacha Pass Pine Island San Carlos Bay16 3. 2.2 Residual Analysis

Analysis of the residuals suggested that when the residual deviation was over 50% of the observed light attenuation, chlorophyll had the highest average relative contribution

to the total K d ( Fig ure 5 )

. Conversely, samples where model predictions were less than

50% of the observed K d had the lowest percent contribution of chlorophyll and the highest percent contribution of the intercept. Turbidity contributed nearly identically irrespective of the pr ediction errors. Examination of the residuals plotted against water quality and field parameters suggested that the time of sample, total depth, nitrogen and phosphorus concentrations and turbidity exhibited little influence on prediction errors in

either upper Charlotte Harbor segments (Fig ure 6.) or lower Charlotte Harbor segments (Fig ure 7.). However, higher chlorophyll and color values tended to correspond with over prediction of the model. Most notable was that positive prediction error s increased

wi th increasing chlorophyll a concentrations above ca. 10 μg/l and trended in an exponential manner as chlorophyll concentrations increased above ca. 30 μg/l

.

F igure 5. Contributions of model constituents to the total light attenuation when prediction errors are at

least 50% greater than t he observed K d (Over), at least 50% less than observed K d (Under), or with 50% of

the observed K d (Avg). The exact proportion is inset in the histograms. 0.28 0.27 0.35 0.35 0.31 0.31 0.14 0.13 0.14 0.24 0.29 0.20

0% 20% 40% 60% 80% 100%

Avg Over Under Intercept Color Turbidity Chla17 Figure 6. Prediction errors plotted as a function of water quality parameters in Upper Charlotte Harbor. The x axis for chlorophyll a ( μg/l) and color (PCU) are plotted on a log base 2 scale for

clarification.18 Figure 7. Prediction errors plotted as a function of water quality parameters in Lower Charlotte Harbor. The x axis for chlorophyll a (μg/l) and color (PCU) are plotted on a log base 2 scale for

clarification.19 Bokeelia, Cape Haze , Pine Island Sound and Lower Lemon Bay had the highest reliability with respect to model predictions and San Carlos Bay, Matlacha Pass, Tidal Peace and Tidal Myakka were the le ast reliable ( F igure

. 8 ). Bokeelia, Cape Haze , Pine

Island Sound and Lemon Bay are largely influence d by coastal gulf waters and less

influence d by direct freshwater inputs than other segments. Conversely, the Tidal

Peace , and Tidal Myakka are largely inf luenced by freshwater inflows and had the highest average concentrations of total phosphorus, total nitrogen and total organic

carbon

. San Carlos Bay is a dynamic estuarine environment heavily influenced by both

the Caloosahatchee River and the Gulf of Mex ico.

3. 3 Model Tuning

Segment

- specific models fit the observed data better than the McPherson and Miller equation in 6 of the 12 segments including East Wall, Tidal Myakka, Tidal Peace, West Wall San Carlos Bay and Tidal Caloosahatchee ( Table 6 .) . Inter estingly, in none of these segments was chlorophyll a significant contributing factor to prediction of

observed K d . In some cases, total phosphorus was a significant contributor to the final segment specific model. However, only in West Wall was the R 2 gr eater than 0.50 indicating that

, in the majority of the segments

, less than half of the variation in K d was explained by the model. Aggregating the data monthly increased the fit to the observed

data in many segments but there remained s ubstantial d isagre ement when compared to optical model predictions based on aggregated water quality data . Further, chlorophyll was no longer a significant predictor of light attenuation in any segment when averaging segment specific monthly values.20 Figure 8. Mean Square Error (MSE) of the predicted and observed K d (top) and coefficient of variation (CV; bottom) for each segment in the CHNEP study area.21 Table 6. Comparison of Coefficient of Determination (R 2 ) for optical model,
segment spe cific regression model and aggregated (monthly averaged) regression model on observed light attenuation ( K d

). For empirical regression results, constituents explaining a significant portion of the

variation in K d are provided and key is provided as footnot e.

Segment Predicted vs

Observed

R 2 Segment Specific Regression Monthly Averaged Segment Specific Regression

Cape Haze 0.26 Color, Turb, TP

R 2 = 0.25 Color

R 2 = 0.40

East Wall 0.26 Color, Turb

R 2 = 0.37 Color, Turb

R 2 = 0.51

Lemon Bay 0.17 Color, Chla, Turb

R 2 = 0.16 Color

R 2 = 0.07

Tidal Myakka 0.07 Color, Turb

R 2 = 0.29 Color

R 2 = 0.45

Tidal Peace 0.14 Color, TP

R 2 = 0.46 Color, TP

R 2 = 0.68

West Wall 0.27 Color, Turb, TP

R 2 =0.56 Color,Turb, TP

R 2 = 0.74

Bokeelia 0.28 Color, Chla, Turb

R 2 =0.29 Color

R 2 = 0.49

Estero Bay 0.13 Color, Turb

R 2 =0.14 Turb

R 2 = 0.09

Matlacha Pass 0.02 NS NS

Pine Island

Sound 0.12 Turb

R 2 =0.02 NS

San Carlos Bay 0.02 Color, TP

R 2 =0.22 Color, TP

R 2 = 0.35

Tidal

Caloosahatchee 0.24 Color, Turb, TN

R 2 =0. 32 Color, TN

R 2 = 0.47
NS = not significant (alpha=0.05) Color=Color (PCU), Turb=turbidity (NTU), Chla = Chlorophyll a (μg/l), TP = Total Phosphorus (mg/l)



## 4.0 D ISCUSSION

The water quality targets developed by the CHNEP are an important contribution to identifying thresholds in water quality that may affect the health and productivity of valued natural resources in the Charlotte Harbor Estuary. Corbett and Hale (2006) established segment specific K d targets and used the empirical data to estimate

thresh old values for water quality constituents that contribute to light attenuation in these segments as a management strategy . One component of th is management strategy is simply to assess the frequency of K d target exceedances and establish

criteria to dete rmine whether that frequency is sufficiently low to allow for seagrass22 success. From this perspective, our analysis has shown that in East Wall, Lemon Bay, Tidal Myakka and Pine Island Sound the model may serve this purpose adequately as there was good a greement between modeled and observed K d at the target values

. However, this does not suggest that the optical model and observed data agr e ed across the range of K d . In fact, in most segments there was substantial disagreement between

modeled and observ ed estimates of K d . Many segments in the Upper Charlotte Harbor region exhibited model over

- prediction bias. These obse r vations tended to occur when chlorophyll contributed a higher relative proportion to the total K d than other

observations. Conversely, u nder prediction bias occur red when the contribution of the intercept was highest and the contribution of chlorophyll was lowest. This suggests that some factor outside the model domain may be contributing to light attenuation in these

circumstances.

M cPherson and Miller (1994) estimated that , on average, 5 5 % of the total light

attenuation was due to non

- chlorophyll suspended matter (NSM) in Charlotte Harbor.
However, the optical model equation does not directly include NSM. Inclusion of turbidity in th e model was intended to represent a scatter coefficient . However, t urbidity represented only 19% of the total contribution to light attenuation on average (McPherson and Miller 1994). The scattering property of estuarine waters is

conditional

, based on th e concentrations of the various water quality constituents in the water at the time of the sample

. In the optical model, that portion of the contribution of

non

- chlorophyll suspended matter not accounted for by turbidity was partitioned into the intercept based on subtraction and is therefore a constant despite NSM having been documented to vary substantially spatially and seasonally in Charlotte Harbor (Dixon and Kirkpatrick, 1999). Th ese factors are likely to be in part responsible for the un d er predicti on of light attenuation, especially in the dry season when color and chlorophyll a

values tend to be lower but NSM may be higher due to winds, tides and vessel traffic

. Bowers and Binding (2006) suggested that reflectance of suspended particles increases

m ultiplicatively with turbulence. Lawson et. al., (2007) suggested wind driven sediment suspension is the dominant source of light attenuation in shallow coastal lagoons. Much of the Charlotte Harbor study area is an integral part of Florida ’s of the Int ra coastal Waterway (ICW) providing an inshore route for vessel traffic. H igh vessel traffic

, especially th ose utilizing the ICW as an inshore route to southern cruising grounds during the winter may also contribut e to the prediction errors by re

- suspending

s ediments into the water column.

While this exercise assumed that the observed K d was measured without error, that is likely not the case. Kirk (1994) describes major sources of measurement error of underwater irradiance as: wave action; atmospheric cond ition, and perturbation of the light field by the vessel. While efforts were made to account for these various factors affecting in situ measurements of light, there is no way to eliminate these factors. Wave action can focus the light field causing rapid temporal intensity changes as the waves pass through the measurement field. The fluctuations are greater in shallow waters than deep waters. However, residual plots suggested that total sample depth did not have a systematic effect on prediction errors in this study. Neither did the time of the sample or the salinity gradient to a large extent. Rather

, it appeared that chlorophyll and color23 values were principally responsible for observation where over prediction was prevalent. The probabilistic nature o f the sampling design likely also contributed to the prediction

errors. M any sampling programs measuring light attenuation empirically use fixed station monitoring programs with station locations along the deep edge of a seagrass

transect. Fixed locations eliminate one source of variability between measurements

relative to probabilistic designs though they are less well generalized to describe a given water body considered for management actions. Phytoplankton is a well documented attenuator of light (Kirk 1994) but results of this study suggest that the McPherson and Miller optical model may overweight the contribution of chlorophyll to the prediction of light attenuation in the Charlotte H arbor study area when chlorophyll a concentrations are greater than 10 μg/l

. The observed under prediction is speculated to come from some unmeasured quantity including the potential for multiplicative interaction among water quality constituents in the water column.



## 5.0 M ANAGEMENT R ECOMMENDATIONS

The CHNEP has estab lished a foundation of objective, science

- based, decision making tools for use as indicators of estuarine health and is furthering its goals under its Comprehensive Conservation and Management Plan to protect and restore water quality through rigorous anal ysis of its management tools. This study has furthered those objectives by assessing the optical model performance relative to empirical estimates of light attenuation. The extent of seagrass in the CHNEP study area is an exceptionally valuable natural re source and a primary focus of the CHNEP Comprehensive Conservation and Management Plan. The continued focus on science based management tools for seagrass will help to ensure the protection of these vital resources as anthropogenic pressures increase. This analysis suggests that m ore efforts are needed to understand the interactions between attenuators of light in these waters before the optical model can be confidently used to set management level criteria for individual water quality constituents in the C harlotte Harbor study area.

In light of the uncertainty in linking water quality and light attenuation in Charlotte Harbor estuarine waters, we sought to derive water clarity target s that w ere relevant to the

observed condition s affecting seagrass within each Harbor segment without explicitly identifying the light requirements of seagrass. The following reasoning was used to derive the proposed water clarity targets:

**•** Mechanistic relationships between ambient/antecedent water quality conditions

a nd the li ving resource requirements of seagrass are not fully understood.

**•** Stability in measures of seagrass areal extent over recent history suggests that

either :
1. Ambient water quality conditions are sufficient for success of seagrasses (as expressed as areal exte nt) within the segment,24 2. seagrasses are stressed by ambient/antecedent water quality conditions but the seagrasses have not expressed the stressor

- response relationship as a change in areal extent, or

3. Ambient/antecedent water quality conditions are not relevant to the success of seagrasses (as expressed as areal extent), or

The preponderance of evidence suggests that water quality, explicitly water clarity, is a limiting factor in determining the depth distribution of seagrass . T herefore

, the third

ar gument is dismissed

. T he second alternative is plausible but the targets identified by this study are intended to make inferences regarding the extent of seagrass within a segment and not on :

**•** Speciation of seagrass within a bed

**•** Density of seagrass within a bed

**•** The quality of seagrasses within a bed

These measures of seagrass condition are better estimated through other monitoring

efforts

.

Based on the above, the following water clarity targets are proposed based on the assumptions that;

**•** changes in t he areal extent of seagrasses are related to changes in water quality even if the mechanistic relationships are not fully understood

, and

**•** i mproving water clarity will result in an increase in the areal extent of seagrasses given other factors are not limi ting.

Given the definitions above, the seagrass targets identified in Task 2 of this scope of work (provided for convenience in Table 7) were used to establish the “target” water clarity condition s for the Harbor segment s . Based on the seagrass targets, t he following

decision rule s were applied:

**•** If the protection target wa s chosen as the segment specific seagrass target,

then the water clarity target established will be a “hold the line” strategy to

maintain ambient conditions experienced over the recent areal surveys

.

**•** If the restoration target wa s chosen as the segment specific seagrass target,

then the water clarity target will be a n “Improvement” strategy measured as an

“ improving ” trend in for light attenuation

.

The tidal tributary seagrass targets i ncluding the Tidal Peace, Tidal Caloosahatchee, Tidal Myakka and Dona and Roberts Bay were not to be considered as management25 targets based on the subcommittee opinion that the influence of tanic river waters

reduced the ability to capture the bottom profi le of these segments with aerial photography as well as the local observations of sparse but substantial coverage of seagrass in areas previously characterized by aerial photography as being devoid of

seagrass. Despite the lack of seagrass targets, the “ Pr otection ” strategy was applied to water clarity in the tidal tributary segments

.

Table 7

. Draft CHNEP Seagrass Targets

Harbor Segment Baseline, adjusted (B) Mean Annual

Extent all years (A) Protection Target Restoration Target Total Target Target Range

Dona and Roberts Bay 112 91 91 21 112 70

- 124

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

- 1,175

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

- 2,597

Tidal Myakka River 344 456 456 456 331

- 539

Tidal Peace River 975 384 384 591 975 295

- 573

Wes t Wall 2,106 1,907 1,907 199 2,106 1,676

- 2,121

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

- 3,591

Cape Haze 5,670 6,998 6,998 6,998 6,709

- 7,464

Lower Charlotte Harbor 2,964 3,342 3,342 3,342 3,101

- 3,520

Pine Island Sound 23,757 26,837 26,837 26,837 2 5,941

- 29,204

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

- 7,619

San Carlos Bay 3,118 4,372 4,372 4,372 3,709

- 5,376

Tidal Caloosahatchee 93 87 87 6 93 2

- 103

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

- 3,409

TOTAL 59,776 62,103 62,103 3,954 66,05 7 N/A

5.1 Target Identification:

A unifying evaluation strategy was conceptually defined to establish and assess water clarity targets for both the protection and the restoration targets . The concept is based on two points in the distribution of light attenuation measurements between 2003 and 2007 that corresponded to the targets identified by CHNEP 2006 and in Corbett and Hale (2006) as well as the grand average value between 2003

- 2007

. For future

reference we call this the “benchmark” distribution. F or example, in Pine Island Sound,

CHNEP identified a K d target of 0.6 (1/m) and the grand average K d between 2003 and 2007 was 0.98 (1/m) as shown in the cumulative distribution function (CDF) plots of Figure 8

. These two points along the benchmark distri bution correspond to the 28 th and

58 th percentile of the empirical distribution of K d between 2003

- 2007. Therefore, we expect that ca.30% of the K d values in any year would be below 0.60m

- 1 and ca. 60%

of the values would be below 0.98m

- 1. If for example, only 15% of the values were

below 0.60m

- 1 and only 40% of the values were below 0.98 for a particular years worth

of data then light attenuation is higher and water clarity is reduced. The converse is also26 true. This can be tested statistically to provide confidence that the se differences are not

due to chance.

Figure 8. Cumulative distribution of K d values in Pine Island Sound between 2003 and 2007 with the CHNEP target value denoted as gray dot and the grand average denoted as a black dot.

P lots for the CHNEP target values and the grand average are provided for each segment in Figures 9

- 11 and the seagrass aerial extents are inset in each figure. Generally, the CHNEP targets occurred near the 30 th percentile and the grand average

occurred between the 60 th and 70 th percentile of the benchmark distribution. Exceptions were West Wall and East Wall where the CHNEP targets were very similar to the grand

average.27 Figure 9. Cumulative **K d**  distributions (2003

- 2007) for Harbor segments with R estoration targets. Benchmark values on distributions are identified by gray dot (CHNEP target) and black dot (Grand average value). Histograms displaying extent of seagrass for each survey year are inset. Upper Lemon Bay targets based on data from 1998

- 2007.28 Figure 10 . Cumulative **K d**  distributions (2003

- 2007) for Harbor segments with Protection targets. Benchmark values on distributions are identified by gray dot (CHNEP target) and black dot (Grand average value). Histograms displaying extent of seagrass for each survey year are inset.29 Figure 11 . Cumulative **K d**  distributions (2003

- 2007) for Harbor Tidal River segments

. Benchmark values on distributions are identified by gray dot (CHNEP target) and black dot (Grand average value). Histograms displaying exte nt of seagrass for each survey year are inset.

Based on the observation that these two points generally aligned with the 30 th and 70 th

percentiles of the benchmark period distribution , these were chosen as points to evaluate each annual years worth of wat er clarity data. The rationale of choosing these particular points along the distribution included:

**•** choosing consistent endpoints among segments would achieve internal consistency in reporting among segments;

**•** The 30 th and 70 th percentiles were in general proximity to the CHNEP targets and the historic averages, respectively;

**•** the 30 th and 70 th percentiles are not likely to be effected by extreme
observations, and

**•** the 30 th and 70 th percentiles are likely to vary independently of one another relative to point s closer together on the distribution curve.

The curve between the 30 th and 70 th percentile values tended to be fairly flat in the CDF plots for both the restoration and protection targets indicating that relatively large30 changes in the exceedance percent iles could be accomplished with small changes in

the K d value. This is an important consideration. Since K d represents an exponential loss of light, small decreases in the K d value result in exponential increases in light penetration to the seagrasses. This strategy is then aimed at maximizing the return on improving water clarity conditions in terms of the increasing the duration of acceptable light penetration to protect and restore seagrass areal extents in each Harbor segment.

These “benchmark poi nts” for each Harbor segment, identified from the distribution of measurements collected over the benchmark time period are provided in Table 8.

Table 8. Segment specific empirical light attenuation K d (m - 1 ) values for the 30 th

percentile and 70 th perc entile based on data collected between 2003

- 2007.

Segment 30 th Percentile 70 th Percentile

Bokeelia 0.58 1.16

Cape Haze 0.63 1.15

Dona and Roberts Bay 0.64 1.04

East Wall 0.64 1.16

Estero Bay 0.91 1.58

Lower Lemon Bay 0.73 1.12

Matlacha Pass 0.73 1.63

Pine Island Sound 0.64 1.1

San Carlos Bay 0.73 1.16

Tidal Caloosahatchee 1.58 2.93

Tidal Myakka 1.3 2.27

Tidal Peace 1.06 2.4

Upper Lemon Ba y ** 0.73 1.18

West Wall 0.73 1.36

** Note: Upper Lemon Bay data are from the 1998

- 2007 time period.

5.2 Assessment:

The binomial test (Wackerly et. al., 1996) will be used to evaluate each year’s water quality data at the benchmark point s on the distribution. For example :

**•** If more than 30% of the K d measurements are below the 30 th percentile benchmark with statistical significance (alpha=0.05) , then the water clarity is considered to be improving and is assigned a value of positive 1.

**•** If less than 30% of the values are below the 30 th percentile benchmark with statistical significance (alpha=0.05) , then the water clarity is considered to be degrading and is assigned a value of negative 1.

**•** Otherwise the value is 0.31 This scoring is pe rformed on both endpoints (i.e. the 30 th and 70 th percentile).

The sum of these score will be used as the basis for the assessment of water clarity for each Harbor segment. The distribution of potential scores ranges from

- 2 to 2

.

For the protection targ ets the following grading system will be used:

Green = s cores greater than

- 1 Stable

Yellow = a s core of

- 1 or less Caution

Red = a score of less than

- 1

f or consecutive years Degrading

For the restoration targets the followin g grading system will be used:

Green = s cores greater than 1 Improving towards target

Yellow = s cores between

- 1 and 1 Caution

Red = a score of less than

- 1 Degrading

As an example, consider the Bokeelia segment (Figure 12). The b enchmar k distribution is defined by the solid black line with the benchmark points represented at the 30 th and

70 th percentiles. Overlaid on this figure are the distributions for 2003 and 2007. The

distribution for 2003 was above the benchmark distribution and th e specific value used

to assess the 30 th percentile was exceeded a larger percentage of the time (i.e., there

were fewer observations at or below the 30 th percentile value). This difference in frequency was statistically significant and therefore was given a score of negative one. Conversely

, in 2007 there were significantly more than 30 percent of the values below

the 30 th percentile value and the score was positive one. Evaluation at the 70 th

percentile values suggested that the exceedance frequencies wer e not significantly

different from the benchmark period and were therefore given a s c ore of zero.32 Figure 12. Benchmark distribution of light attenuation in Bokeelia with data from 2003 and 2007 overlaid providing an example of the scoring algorithm.

An example of the scoring algorithm applied each year of the benchmark period applied

to Cape Haze and Pine Island Sound is provided in Figure 1 3 . The figures are

constructed so that the b enchmark period is a solid black line and each individual years

dat a are overlaid with broken line of different colors. The scores for each benchmark are provided as an inset table and the resulting grade is given for the cumulative scores f or each year. In Cape Haze

, 2003 had significantly fewer observations below the P3 0 value and in 2004 both the P30 and P70 values occurred less frequently as well resulting in negative scores and a grade of “ degrading ” condition because the score was negative one or less for consecutive years for this protection target. Conversely in

20 07 nearly 60 percent of the observations were below the P30 threshold, indicating a higher frequency of good water clarity conditions. For this year, both the P30 and P70 were improved compared to the benchmark time period and consequently the grade is

sta ble water clarity for that year. In Pine Island Sound, water clarity was stable over the entire time period and therefore all grades are green in color. The importance of stability in water clarity condition may be an extremely important characteristic for the long term success of seagrasses. Pine island Sound has far more seagrass than any other segment and also has the most consistent water clarity over the benchmark period.33 Figure 1 3 . Cumulative distribution of light attenuation for benchmark period (solid black line) with benchmark points and each individual years data from 2003

- 2007. Scores are inset.34 Based on th is grading system , the restoration targets have more stringent water quality criteria than the protection targets. Stability in scores re lative to the benchmark period is considered sufficient for the protection targets but not for the restoration targets.
Therefore, scores between

- 1 and 1 are given a “caution” score. These scores can be related to changes in seagrass over time by either a dding the scores between the biennial seagrass surveys, or evaluating each of the benchmark scores (i.e., the 30 th

and 70 th percentile) separately. It should be noted that the binomial test used to score the water clarity data rel ies on the assumption that samples are independent and the design of the CCHMN network conforms to this assumption. The test result also relies on the sampling frequency such that dramatic changes to the sampling design may affect the power of the binomial test to distinguish a sig nificant result.

Based on the above assessment, i t is recommended that in 2012 , the scoring method

be re

- assessed to ensure that the benchmark p eriod remains relevant to the expected ambient water quality conditions in each Harbor segment. A change in the method used to collect information on light attenuation occurred recently and it will be important to ensure that this change in method did not affect the distribution of values. The grading system should also be evaluated at this time to determine the se nsitivity of the grading cutpoints relative to changes in water clarity and seagrass conditions and consideration should be given to using the identical scoring algorithm to assess the modeled K d estimates from McPherson and Miller (1994) and compared thos e scores to the

observed values.

The fourth task of this project is to update the nutrient loading estimates for all sub basins of the CHNEP study area. These pollutant loading estimates will be an important contribution to the future development numeri c nutrient criteria for the estuarine portions of the CHNEP study area. Numeric nutrient criteria will establish target loadings affecting water quality in the estuaries, again using seagrass as a principal natural resource requiring protection. The combin ation of the water clarity targets developed in this report, pollutant loading estimates identifying major contributing sources to the Harbor, and the development of numeric nutrient criteria will contribute to the effective management of the CHNEP study a rea to help achieve the goals set forth in the CHNEP’s Comprehensive Conservation and Management Plan.35 

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