CHARLOTTE HARBOR NATIONAL ESTUARY 

PROGRAM 

NUMERIC NUTRIENT CRITERIA 

Task 10 Dissolved Oxygen 

Draft Letter Memorandum 

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 

May 26, 2011
i 

Table of Contents 

LIST OF FIGURES .....................................................................................................................................II

LIST OF TABLES ......................................................................................................................................IV

FOREWORD ............................................................................................................................................ V

ACKNOWLEDGMENTS ...........................................................................................................................VI

EXECUTIVE SUMMARY ......................................................................................................................... VII

1.0 INTRODUCTION AND OBJECTIVES ........................................................................................ 1-1

2.0 BACKGROUND ....................................................................................................................... 2-1

3.0 DATA SOURCES ....................................................................................................................... 3-1

4.0 APPROACH ............................................................................................................................. 4-1

5.0 RESULTS .................................................................................................................................. 5-1

5.1 TEMPORAL PATTERNS IN DO EXCEEDENCES .................................................................................. 5-1

5.2 SPATIAL PATTERNS IN DO EXCEEDENCES .................................................................................... 5-18

5.3 FACTORS AFFECTING DO EXCEEDENCES .................................................................................... 5-23

6.0 CONCLUSIONS ....................................................................................................................... 6-1

7.0 LITERATURE CITED ..................................................................................................................... 1
ii

List of Figures 

Figure 1-1. CHNEP Bay Segments and Water Management District Boundaries. ............................... 1-2

Figure 3-1. Sarasota County ambient water quality sampling station locations.................................... 3-2

Figure 3-2. PRMRWSA, SFWMD, and FIU ambient water quality sampling station locations. ............. 3-3

Figure 3-3. CCHMN, City of Cape Coral and Lee County ambient water quality sampling station 

locations........................................................................................................................... 3-4

Figure 3-4. FFWCC water quality sampling station locations............................................................... 3-5

Figure 3-5. Number of total DO observations, Dona and Roberts Bays. .............................................. 3-6

Figure 3-6. Number of total DO observations, Upper Lemon Bay........................................................ 3-6

Figure 3-7. Number of total DO observations, Lower Lemon Bay........................................................ 3-7

Figure 3-8. Number of total DO observations, Tidal Myakka River. ..................................................... 3-7

Figure 3-9. Number of total DO observations, Tidal Peace River. ....................................................... 3-8

Figure 3-10. Number of total DO observations, Charlotte Harbor Proper. ............................................. 3-8

Figure 3-11. Number of total DO observations, Pine Island Sound. ...................................................... 3-9

Figure 3-12. Number of total DO observations, Matlacha Pass............................................................. 3-9

Figure 3-13. Number of total DO observations, San Carlos Bay. ........................................................ 3-10

Figure 3-14. Number of total DO observations, Tidal Caloosahatchee River....................................... 3-10

Figure 3-15. Number of total DO observations, Estero Bay. ............................................................... 3-11

Figure 5-1. Time series of DO concentrations, Dona and Roberts Bays.............................................. 5-2

Figure 5-2. Time series of DO concentrations, Upper Lemon Bay....................................................... 5-2

Figure 5-3. Time series of DO concentrations, Lower Lemon Bay....................................................... 5-3

Figure 5-4. Time series of DO concentrations, Tidal Myakka River. .................................................... 5-3

Figure 5-5. Time series of DO concentrations, Tidal Peace River. ...................................................... 5-4

Figure 5-6. Time series of DO concentrations, Charlotte Harbor Proper.............................................. 5-4

Figure 5-7. Time series of DO concentrations, Pine Island Sound....................................................... 5-5

Figure 5-8. Time series of DO concentrations, Matlacha Pass. ........................................................... 5-5

Figure 5-9. Time series of DO concentrations, San Carlos Bay........................................................... 5-6

Figure 5-10. Time series of DO concentrations, Tidal Caloosahatchee River........................................ 5-6

Figure 5-11. Time series of DO concentrations, Estero Bay.................................................................. 5-7

Figure 5-12. Percent of DO exceedences by year, Dona and Roberts Bays. ........................................ 5-7

Figure 5-13. Percent of DO exceedences by year, Upper Lemon Bay. ................................................. 5-8

Figure 5-14. Percent of DO exceedences by year, Lower Lemon Bay. ................................................. 5-8

Figure 5-15. Percent of DO exceedences by year, Tidal Myakka River................................................. 5-9

Figure 5-16. Percent of DO exceedences by year, Tidal Peace River................................................... 5-9

Figure 5-17. Percent of DO exceedences by year, Charlotte Harbor Proper. ...................................... 5-10

Figure 5-18. Percent of DO exceedences by year, Pine Island Sound. ............................................... 5-10

Figure 5-19. Percent of DO exceedences by year, Matlacha Pass. .................................................... 5-11

Figure 5-20. Percent of DO exceedences by year, San Carlos Bay. ................................................... 5-11

Figure 5-21. Percent of DO exceedences by year, Tidal Caloosahatchee River.................................. 5-12

Figure 5-22. Percent of DO exceedences by year, Estero Bay. .......................................................... 5-12

Figure 5-23. Percent of DO exceedences by calendar month, Dona and Roberts Bays. ..................... 5-13

Figure 5-24. Percent of DO exceedences by calendar month, Upper Lemon Bay. .............................. 5-13

Figure 5-25. Percent of DO exceedences by calendar month, Lower Lemon Bay. .............................. 5-14

Figure 5-26. Percent of DO exceedences by calendar month, Tidal Myakka River.............................. 5-14

Figure 5-27. Percent of DO exceedences by calendar month, Tidal Peace River................................ 5-15

Figure 5-28. Percent of DO exceedences by calendar month, Charlotte Harbor Proper. ..................... 5-15

Figure 5-29. Percent of DO exceedences by calendar month, Pine Island Sound............................... 5-16

Figure 5-30. Percent of DO exceedences by calendar month, Matlacha Pass. ................................... 5-16

Figure 5-31. Percent of DO exceedences by calendar month, San Carlos Bay................................... 5-17

Figure 5-32. Percent of DO exceedences by calendar month, Tidal Caloosahatchee River. ............... 5-17

Figure 5-33. Percent of DO exceedences by calendar month, Estero Bay. ......................................... 5-18

Figure 5-34. Distribution of DO values in each of the CHNEP segments............................................. 5-19
iii

Figure 5-35. Spatial distribution of DO during summer months (June-September) for the northern portion 

of the CHNEP area......................................................................................................... 5-20

Figure 5-36. Spatial distribution of DO during summer months (June-September) for Tidal Myakka, Tidal 

Peace, and Charlotte Harbor Proper............................................................................... 5-21

Figure 5-37. Spatial distribution of DO during summer months (June-September) for the southern portion 

of the CHNEP area......................................................................................................... 5-22
iv

List of Tables 

Table 5-1. Summary of DO observations by segment for the months June through September. ............ 5-22

Table 5-2. Logistic regression parameter estimates including odds ratios, significance levels, and overall 

model goodness-of-fit (Hosmer and Lemeshow). The response variable is the probability of a 

bottom DO < 4 mg/l. ..................................................................................................... 5-24

Table 5-3. Summary statistics of stratification (bottom salinity – surface salinity) by segment. ............... 5-25

Table 5-4. Summary of DO observations by segment for the months June through September. ............ 5-26
v 

FOREWORD 

This report was prepared by Janicki Environmental, Inc. for the Charlotte Harbor 

National Estuary Program in fulfillment of Task 10 of the Water Quality Target 

Refinement Project. 
vi

ACKNOWLEDGMENTS 

Financial support for this project was provided by the Charlotte Harbor National Estuary 

Program, the Southwest Florida Water Management District, and the South Florida 

Water Management District. We wish to thank the many participants of the Technical 

Advisory Committee and Water Quality Quantifiable Objectives sub-committee meetings 

that led to the development of this process. We are grateful for the data collection 

efforts of the Coastal Charlotte Harbor Monitoring Network, the Charlotte Harbor 

Volunteer Monitoring Network, Lee County, Charlotte Harbor Aquatic Preserves, Cape 

Coral, Florida International University, The Peace River Manasota Water Supply 

Authority, Sarasota County, and Mote Marine Laboratory. We sincerely appreciate the 

contributions of Keith Kibbey, Peter Doering, Craig Hankins, Rob Johnson, Renee 

Duffy, Mindy Brown, Ray Leary, Ralph Montgomery, Sam Stone, and Kellie Dixon for 

allowing access to their data. Finally, we thank Lizanne Garcia and Kris Kaufman of the 

Southwest Florida Water Management District, Kevin Carter and Peter Doering of the 

South Florida Water Management District, and Lisa Beever, Liz Donley, and Judy Ott of 

the Charlotte Harbor National Estuary Program for supporting this work. 
vii 

EXECUTIVE SUMMARY 

The objective of this task was to characterize the dissolved oxygen levels in the 

segments of the Charlotte Harbor National Estuary Program area, assess principal 

drivers of DO exceedances, and evaluate the relevance of the empirical distribution of 

dissolved oxygen concentrations to the Florida Department of Environmental 

Protection’s impaired Water Rule standard for dissolved oxygen with respect to the 

development of recently proposed numeric nutrient criteria for the Charlotte Harbor 

National Estuary Program area (Janicki Environmental, 2011). This assessment 

included a descriptive characterization of the spatial and temporal attributes of observed 

dissolved oxygen concentrations. 

 The following conclusions can be drawn from the analyses and results from this task: 

 The empirical evidence presented above suggests that the majority of CHNEP 

segments are meeting full aquatic life uses with respect to DO. Six segments 

(Dona and Roberts Bays, Lower Lemon Bay, Charlotte Harbor Proper, Pine 

Island Sound, San Carlos Bay, and Estero Bay) had no annual DO exceedences. 

Of the five segments that had exceedences, Tidal Myakka and Tidal 

Caloosahatchee had a single exceedence while Upper Lemon Bay, Tidal Peace, 

and Matlacha Pass had three exceedences each. Examination of spatial 

distribution revealed no strong tendencies for DO less than 4 mg/l. However, the 

probability of DO values less than 2 mg/l was highest in the Tidal Peace and the 

upper portion of Charlotte Harbor Proper. Previous work by Camp, Dresser & 

McKee (1998) revealed that stratification was more prevalent when low DO 

concentrations occurred in the Tidal Peace and Charlotte Harbor. Logistic 

regression models developed for this report confirm that stratification is one of 

the principle drivers of DO exceedences in the Tidal Peace and Charlotte Harbor. 

 The principal factor affecting DO in the segments of the CHNEP is temperature. 

This fact is evident in both the descriptive time-series plots and the results of 

ordinary least-squares regression. 

 Additional models were developed to identify the explanatory variables that 

contribute to the probability of DO exceedences at the segment level. In all 

segments, temperature is the primary factor that is positively associated with a 

DO exceedence (a DO concentration < 4 mg/l). Though chlorophyll is included in 

the models of three segments (Tidal Myakka, Pine Island Sound, and Tidal 

Caloosahatchee), in Tidal Myakka and Tidal Caloosahatchee an increase in 

chlorophyll leads to a decrease in the probability of a DO exceedence. This 

contradicts the conceptual model proposed by FDEP that excess nutrients from 

anthropogenic assaults result in algal blooms which result in increased organic 

deposition and decomposition which in turn lead to reduced DO concentrations. 
viii 

 There was evidence of a lack of fit in the models developed for several of the 

segments, therefore additional models were developed for these segments. 

These models estimate the probability of a bottom DO less than 4 mg/l as a 

function of several explanatory variables, including salinity stratification. There 

was no evidence of a lack of fit in the additional models. Temperature and 

stratification were the main drivers of DO exceedences in Tidal Peace and 

Charlotte Harbor Proper. Chlorophyll was not a significant predictor of bottom 

DO exceedences in either of the segments. 

 Based on the weight-of-evidence presented here, it is reasonable to conclude 

that the proposed numeric nutrient criteria are protective of full aquatic life uses 

with respect to DO. 
1-1 

1.0 INTRODUCTION AND OBJECTIVES 

The Charlotte Harbor National Estuary Program (CHNEP) has recommended numeric 

nutrient criteria to U.S. Environmental Protection Agency (EPA) for Dona and Roberts 

Bays, Upper Lemon Bay, Lower Lemon Bay, Tidal Myakka River, Tidal Peace River, 

Charlotte Harbor Proper, Pine Island Sound, Matlacha Pass, San Carlos Bay, Tidal 

Caloosahatchee River, and Estero Bay (Figure 1-1). The criteria, as proposed to EPA, 

are segment-specific and are expressed as annual total nitrogen (TN) and total 

phosphorus (TP) concentrations and loads using chlorophyll a concentrations as a 

primary response variable (Janicki Environmental, 2011a; 2011b). An integral 

component of the establishment of numeric nutrient criteria involves the assessment of 

protecting full aquatic life support within the estuary. This investigation examines the 

characteristics of dissolved oxygen concentrations in CHNEP segments with respect to 

the Florida Department of Environmental Protection’s (FDEP) dissolved oxygen 

standard of 4 mg/l as part of that process. The FDEP has established the state water 

quality standards (FAC 62.302) to protect the designated uses of Florida waterbodies. 

The standard established for DO in predominantly marine waters requires meeting the 4 

mg/L standard no less than 90% of the time (i.e., a 10% exceedance). Dissolved 

oxygen is also used as an additional indicator of eutrophic conditions and can serve as 

an indicator of habitat suitability for a wide range of aquatic fauna (e.g., fishes and 

benthic invertebrates) (USEPA, 2001). 

The conceptual model applied by FDEP in establishing the DO standard is that excess 

nutrients from anthropogenic assaults result in algal blooms which in turn result in 

increased organic deposition and decomposition which in turn lead to reduced DO 

concentrations. There are several case studies that support that excess nutrients from 

poorly treated municipal wastewater as well as non-point source runoff have contributed 

to eutrophic estuarine conditions. Symptoms of eutrophication include excess primary 

production, deposition and decomposition of phytodetritus and consequently increased 

biological oxygen demand which reduces the DO content of estuarine waters (Nixon, 

1995). The objective of this effort was to assess the percentage of state standard 

exceedances in DO and assess drivers of DO exceedances in the segments of the 

CHNEP area with respect to the development of recently proposed numeric nutrient 

criteria for the CHNEP area (Janicki Environmental, 2011a; 2011b). This study also 

explores evidence that the FDEP conceptual model described above is currently 

relevant in the CHNEP segments. In particular, this assessment investigated the 

relationship between the percentage of DO exceedances in each of CHNEP segments 

and the threshold values for chlorophyll a established as part of an overall nutrient 

control strategy (Janicki Environmental, 2011a). Descriptive and quantitative analyses 

were used to evaluate the effects of known drivers of DO including temperature, color, 

stratification, and chlorophyll a concentrations. 
1-2 

Figure 1-1. CHNEP Bay Segments and Water Management District Boundaries. 
2-1 

2.0 BACKGROUND 

Cultural eutrophication, which is nutrient excess leading to overproduction of microalgae 

and associate trophic imbalances, is common in estuaries near human population 

centers. Under conditions of eutrophication DO may exhibit extreme diel cycles. 

Photosynthesis via algae production elevates DO levels in the water during the day. 

However, at night when respiration is high, DO levels can drop dangerously low. 

Eutrophication can also lead to periodic or long term hypoxia (water column oxygen 

concentrations <2 mgl) and anoxia in estuarine ecosystems. Fishes, crabs and shrimp 

will attempt to move away from oxygen concentrations of less than 2 mgl and few 

marine animals survive in prolonged exposure to hypoxic conditions. DO levels are 

often quite variable in estuarine systems due to fluctuations in temperature, salinity, 

basin morphology, and overall productivity. At times, the Charlotte Harbor estuary has 

a significant hypoxic zone that approaches 90 km2 in September (Camp, Dresser, and 

McKee, Inc. 1998). In the following paragraphs, three papers are reviewed which 

address DO in Charlotte Harbor, Florida.

The first report was written by Camp Dresser and McKee detailing a study initiated by 

the Surface Water Improvement & Management (SWIM) Department of SWFWMD to 

determine the historic and present extent of hypoxia in upper Charlotte Harbor and to 

determine the potential future extent of hypoxia in the upper harbor. The project had 

five main goals:

1) Estimate the occurrence of hypoxia at a reference station using historical 

data; 

2) Implement a monitoring program to define the relationships between the 

bottom water dissolved oxygen at the reference station and stations 

distributed through the upper harbor; 

3) Characterize the onset and spread of a hypoxic event; 

4) Evaluate the relationship between stratification and hypoxia; and, 

5) Propose and evaluate conceptual models of the cause of oxygen depletion 

leading to hypoxia.

Sampling was coordinated by Mote Marine Laboratory and sampling was conducted in 

1996 on 10 sampling dates from September 16 through November 12. Sampling was 

completed at 16 stations and visited twice during each visit, with vertical profiles of 

temperature, salinity, and dissolved oxygen collected at 0.5 m intervals. Samples were 

also collected for color and secchi depth readings were taken. One station in the upper 

harbor was designated as a “reference station” and was visited more frequently during 

each sampling day. The data set contained over 2,450 values for temperature, salinity 

and dissolved oxygen, with 324 separate station visits. Historical data was reported 

from the Environmental Quality Laboratory (EQL) of Port Charlotte with monthly DO 

data from 1975. 
2-2 

Analysis of historical data showed lower DO concentrations relative to location with 4.0 

mg/L or less observed in the lower Myakka and Peace rivers and upper Charlotte 

Harbor. Lower Charlotte Harbor stations had DO concentrations of 4.0 mg/L or less for 

only 5% or less of total samples. Upper harbor and lower rivers also had hypoxic 

conditions during more months of the year as compared to those in the lower harbor. 

The duration and frequency were related to station location. June through October had 

the most frequent and widespread occurrences of DO concentrations less than 4.0 

mg/L. September had the most widespread hypoxia with seven of the EQL stations at 

2.0 mg/L or less. Comparison of annual data revealed no temporal trend in DO for the 

period 1975 through 1990. 

The authors attempted to estimate the spatial extent of hypoxia from historical data 

based on DO relationships between the reference marker and other locations in the 

harbor, but the model was limited by sample size. The authors noted that during the 

1996 sampling only 27 of 2,093 samples were hypoxic, limiting all observations to a 

single sampling day. As a result, an alternate approach of comparing the relationship of 

hypoxic conditions at the reference site to the other physical and chemical conditions 

was completed. Linear regression techniques were employed to determine the flow 

metric which best explained variation in DO saturation at the reference site. The model 

included cumulative flows of the Myakka and Peace Rivers for the current day and 

seven previous days and had an r2 of 0.55. Possible additional covariates including 

color, nitrate, ammonia, total phosphorus and long term wind data were evaluated. 

Wind and nitrate were not significantly correlated with flow so were included in further 

analyses. Nitrate did not improve the model fit, but cumulative wind for the three 

previous days did. The final model for the reference site included cumulative flows from 

the Myakka and Peace Rivers for the current day and seven previous days, cumulative 

wind for the three previous days, and monthly intercepts. This model explained 56% of 

the variation in bottom DO saturation. 

Using the model that was developed for the reference site as a starting point, the 

authors developed models for the Peace River upstream of the reference station. In the 

first model the authors used a single variable to explain variation in DO saturation. 

Highest correlation was found when Peace River flows for current day and 7 previous 

days were used. Using Peace River flows resulted in an r2 of 0.50. Using other 

variables including ammonia, nitrate, and chlorophyll caused the r2 values to drop 

substantially. In the second model, Peace River flow and a covariate were used. R2

improved only slightly, to between 0.52 and 0.54, for all other variables. These included 

current month nitrate, previous month TP, current month ammonia, and current and 

previous month chlorophyll. 

Additional models were used to investigate the relationship between hypoxic conditions 

and three stations within close proximity to the reference station. Two stations were 

below the reference station in the harbor and the other was in the Peace River. The 

relationship between hypoxia as defined by DO saturation and flow predicted between 

54-67% of the variation within the three stations. After the flow model was developed, 

other parameters including color, ammonia, nitrate + nitrite, total phosphorus and long 
2-3 

term wind data were tested for correlation with stream flow at each station. Color and 

NH3 significantly correlated to flows at all sites and were discarded. Same day TP and 

NO2+NO3 did not improve the model’s fit and were not used. The combination of flow 

and wind data significantly improved the models. The new models with independent 

monthly intercepts predicted between 54-64% of the variation in the bottom DO 

saturation at the three stations. 

A comparison of hypoxia with salinity stratification showed hypoxic conditions were 

accompanied by strong salinity and oxygen stratification on some sampling dates but 

were absent from others. Time series of delta salinity and delta percent saturation 

showed a strong seasonal agreement. Regressions were developed for both the delta 

salinity versus bottom percent DO saturation and for surface minus bottom percent 

saturation. Correlations ranged from 0.36-0.54 for linear, log, power and exponential 

trial fit. While the relationship was significant, the delta salinity only explained 55% of 

the variation.

Potential oxygen sinks were investigated as they relate to residence time, sediment 

oxygen demand (SOD) and biological oxygen demand (BOD) using total system volume 

and flow rates. Flushing rates of around 38 days for summer month were calculated for 

Charlotte Harbor proper. These values agreed with those found by Miller and 

McPherson (1991). The EPA conducted calculations of SOD during the 1980s. The 

range of SOD values in Upper Charlotte Harbor were 1.06-1.49 g O2/m2/d. In the 

absence of external oxygen inputs and a starting water column of 6.0 mg/L of O2, in 6.7 

days the resulting O2 concentrations were calculated to be 2.0 mg/L O2. BOD was 

monitored during limited sampling and averaged 2.1 mg/L. The authors calculated that 

the depletion of O2 from 6 mg/L to 2mg/L would take about 7 days on average, which 

agreed with SOD calculations. Oxidation of algal biomass was also compared using 

date from the WASP model and modeling literature values. The authors assumed an 

algal bloom producing 50 g/l of chlorophyll. Using kinetic rates included in the WASP 

model, daily oxidation consumption would require approximately 19 days for the water 

column to go from 6.0 mg/L O2 to 2 mg/L O2. The lack of SOD and BOD correlation 

was noted with personal communication from A. Janicki, citing attempts to model algal 

cycles in Charlotte Harbor as disappointing. 

Due to the lack of hypoxia, the district extended the monitoring component of the project 

into 1997 with the goal to monitor and understand the spread of hypoxia. On July 24, 

1997, a Hydrolab Datasonde 7 was deployed and set at 15 minute intervals. Transects 

were conducted on July 31, August 4, and August 14 to characterize the spatial extent 

of hypoxia. Analysis of the data revealed that during large shifts in dissolved oxygen 

there was an inverse relationship between oxygen saturation and salinity. Shifts in 

dissolved oxygen occurred rapidly, with over 30% change in the course of several 

hours. Unfortunately, during the July 24 sampling several areas of super-saturation 

were recorded but there was no hypoxia observed.

 

In conclusion, the occurrence of hypoxia in Charlotte Harbor was significantly related to 

flow and wind speed, explaining 50% of the variation bottom water oxygen 
2-4 

concentration. Salinity stratification was also prevalent during times of low oxygen which 

inhibited gas exchange and resulted in persistence of hypoxia through the late summer, 

peaking in September with an average of 34 mi2 of hypoxia. 

Tomasko et al. (2006) investigated dissolved oxygen dynamics in Charlotte Harbor in 

response to Hurricanes Charley, Frances, and Jeanne. The unpredictability of storm 

occurrence, track and strength made directed studies of the impacts of hurricanes 

inherently difficult. Some research projects had studies underway when a hurricane 

impacted their study area, allowing them to measure direct responses from the storm. 

Following Hurricane Andrew, massive fish kills occurred in Everglades National Park, 

possibly from depleted oxygen levels (Tilmant et al., 1994). Hurricane Fran in 1996 

caused severe dissolved oxygen deficits and high contaminant loading near Cape Fear, 

North Carolina, resulting in massive fish kills (Burkholder, 2004) and declines in total 

benthic abundance (Mallin et al., 1999; 2002). In 1999, three sequential hurricanes 

(Dennis, Floyd, and Irene) impacted Pamlico Sound, North Carolina, resulting in strong 

vertical stratification of the water column, bottom water hypoxia and a sustained 

increase in algal biomass (Paerl et al., 2001).

During August and September 2004, three hurricanes impacted the Charlotte Harbor 

watershed. The first hurricane, Hurricane Charley, was a category 4 storm with surface 

winds of 130 knots at landfall. Within the next six weeks, Hurricanes Frances and 

Jeanne struck the east coast of Florida, bringing high rainfall to the Charlotte Harbor 

watershed. In response to water quality concerns, water quality sampling was 

increased from monthly to weekly. Water quality stations locations included Bartow (24 

km), Fort Meade (11km), Wauchula (0 km), Zolfo Springs (4km), Charlie Creek near 

Gardner (6km), Arcadia (0km), Joshua Creek at Nocatee (2km), Peace River WSA 

Intake (0km), Horse Creek near Mayakka Head (26 km), Horse Creek near Arcadia (13 

km), and Charlotte Harbor. The values in parentheses represent the distance from the 

eyewall of Hurricane Charley. Field sampling parameters included temperature, DO, 

and pH. Additional laboratory parameters included turbidity, total suspended solids 

(TSS), color, and biological oxygen demand. 

 

Results showed that close proximity to the eyewall of Hurricane Charley impacted the 

presence of hypoxia. At Fort Meade, Charlie Creek, and Joshua Creek, DO were 

concentrations were hypoxic. In Horse Creek, hypoxia was not found at Myakka Head, 

but it was found at Aracadia with closer proximity to the eyewall. In the upper and 

middle portion of the Peace River, oxygen levels took three months to recover to preCharley levels. All stations had elevated TSS (above the median but below the 

threshold for top 10%), color (all sites had values in excess of 200 PCU), and BOD (five 

of six sites had anoxia values higher than the threshold value for the highest 10% of 

values), indicating high amounts of dissolved organic matter.

 

This paper identified two reasons for increased hypoxia within Charlotte Harbor; 

stratification (Camp, Dresser & McKee, 1998), and increased organic loads (Turner et 

al., 2006). The authors stated that while hypoxia was a common occurrence throughout 

the watershed during the wet season (which coincides with warmer temperatures), the 
2-5 

combined effects of Hurricanes Charley, Frances, and Jeanne resulted in widespread 

hypoxia specifically with close proximity to the eyewall of Hurricane Charley. Increased 

organic material caused increased BOD which lead to hypoxic conditions. Increased 

freshwater flow resulted in salinity stratification which increased the duration of hypoxic 

conditions. Hypoxic conditions in the harbor were resolved within 1 month due to shorter 

residence times as compared to 3 months of hypoxic conditions in the Peace River. 

Turner et al. (2006) investigated water quality changes from 1800 to 2000 in Charlotte 

Harbor using sediment analysis from cores collected from the midsummer hypoxic 

zone. Four sediment cores 10 cm in diameter by 50 cm long were collected by divers at 

<2m depth from two locations. Biological and geochemical proxies were used to 

investigate the occurrence of low oxygen conditions and to hypothesize what caused 

the significant hypoxic zone which approaches 90 km2 in late summer in Charlotte 

Harbor Estuary. Paleo-indicators included biologically bound silica (BSi), which 

measures remnant diatom frustules, a direct measure of productivity. Phytoplankton 

pigments including chlorophyll a were used to examine the phytoplankton community 

and changes within this community. As eutrophication in coastal ecosystems increases 

biological species composition can change from more desired (diatoms) to less desired 

species (cyanobacteria). Carbon sources were evaluated to determine if they were 

terrestrial or in-situ in origin. Total Carbon and nitrogen and percentage organic carbon 

are often expressed as C:N ratios. The quality of organic matter also controls the 

balance between N mineralization or ammonification (the release of NH4-N from 

decomposed organic matter) and incorporation of NH4-N into bacterial biomass 

(Schlesinger 1997). At high C:N ratios, N is sequestered in biomass, whereas at lower 

ratios NH4-N is released. Grain size determines how much organic matter is found 

within the sediments and may be a good proxy of overall ecosystem organic matter. 

Elemental analysis for trace metals were analyzed and included Al, Rn, Pb, Ba, Ca, Cd, 

Cu, Fe, Mn, P, S, Si, and V.

Results of the analyses showed oxygen concentrations in the estuary varied from 

greater than 100% saturation in surface waters to 0% saturation in bottom waters. 

Oxygen concentrations declined from 1975 to 1995 but returned to pre-1975 values by 

1998. The authors found that long-term declines in river flow affected the oxygen 

dynamics by raising salinity which increased stratification. Linear regression analysis 

showed a 3.36% decline in oxygen saturation for a one μg/L increase in chlorophyll a. 

A linear regression between chlorophyll a and total nitrogen yielded an r2 of 0.24. In 

summary, phytoplankton production was related to nitrogen loading and increased N 

loading led to increased oxygen consumption. 

Total carbon and sediment density increased in all cores sampled. Percent organic C 

increased around 1950 which implied greater loading via phytoplankton. Calculations of 

estimated carbon loading demonstrated a carbon accumulation rate of 59 mg C m-3 h-1

for a 2.4 m water column (McPherson et al. 1990). The authors believe this high carbon 

accumulation was from primary production by phytoplankton, although alternate 

explanations could be from allochthonous inputs from terrestrial sources. 

Results from elemental analysis showed increases in S isotopic composition with time, 
2-6 

which was consistent with increased organic loading and reducing conditions with lower 

oxygen concentrations. The concentration of biogenic silica BSi increased from 1900 

onward, which is indicative of pelagic rather than terrestrial sources of organic carbon. 

As BSi increased, δ14 S values became heavier, which may indicate a link between algal 

production and higher sulfate reduction. 

Phytoplankton pigment results showed higher concentrations of flucoxanthin, an 

indicator of diatoms. Zeaxanthin, an indicator of cyanobacteria, were higher in the 

upper sections of the sediments. No cyanobacteria traces were found in Charlotte 

Harbor sediments from 1800-1925, indicating that cyanobacteria were not present in 

Charlotte Harbor during this time.

 

Overall, the authors provided two hypotheses for the rise in organic matter in sediments 

since the 1950s. The first was the “eutrophication” hypothesis which concluded that 

production and deposition occurred from within the water column. The second 

hypothesis was the “watershed” hypothesis which assumed materials washed in from 

allochthonous sources. C:N ratios and δ13C were more consistent with the 

eutrophication hypothesis because of sources of more local origin. The authors used 

an inverse graphing technique and a mixing model, both of which demonstrated 

increases in organic C resulted from algal inputs and not terrestrial origin. In 

conclusion, the authors believe the data showed that phytoplankton in Charlotte Harbor 

estuary were nitrogen limited and nitrogen loading increased. This increase resulted in 

in-situ organic loading which expanded hypoxic water formation during the summer 

months. 
3-1 

3.0 DATA SOURCES 

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

 City of Cape Coral (CCC), 

 Coastal Charlotte Harbor Monitoring Network (CCHMN), 

 Florida Fish and Wildlife Conservation Commission Fisheries Independent 

Monitoring Program (FFWCC), 

 Florida International University (FIU), 

 Lee County (LeeCo), 

 Peace River Manasota Regional Water Supply Authority (PRMRWSA), 

 Sarasota County (SarCo), and 

 South Florida Water Management District (SFWMD).

In addition to the above water quality data, data were available from the Charlotte 

Harbor Estuaries Volunteer Water Quality Monitoring Network. However, DO data from 

the volunteer network were not included in our analyses as the sampling protocol calls 

for samples to be collected at sunrise, often in shallow near shore waters. As noted by 

Duffey et al. (2007), “Because of this sampling design, the results represent the lowest 

daily DO values found following night-time absence of photosynthesis combined with 

community respiration. In addition, shallow, near shore DO results may exhibit low 

values as a result of consumption of oxygen via decomposition of organic materials 

from shoreline vegetation.” 

In total, 48,192 DO observations were analyzed from 19,777 sampling stations in the 

segments of the CHNEP. Several sampling programs use a fixed station sampling 

design (FIU, PRMRWSA, SarCo, and SFWMD) while others use a random sampling 

design (CCC, FFWCC, and CCHMN). Lee County (LeeCo) uses a combination of 

random and fixed station sampling. The Sarasota County water quality sampling station 

locations are presented in Figure 3-1. The fixed station sampling locations from 

PRMRWSA, SFWMD, and FIU are presented in Figure 3-2. The sampling station 

locations for CCHMN, City of Cape Coral, and Lee County are presented in Figure 3-3. 

Lastly, the water quality sampling locations from the Fisheries Independent Monitoring 

of the FFWCC are presented in Figure 3-4. The total number of DO observations in 

each year from 1996 through 2009 is provided for each segment in Figure 3-5 through 

3-15. For convenience, all data in this report are presented from north to south. 
3-2 

Figure 3-1. Sarasota County ambient water quality sampling station locations. 
3-3 

Figure 3-2. PRMRWSA, SFWMD, and FIU ambient water quality sampling station locations. 
3-4 

Figure 3-3. CCHMN, City of Cape Coral and Lee County ambient water quality sampling station 

locations. 
3-5 

Figure 3-4. FFWCC water quality sampling station locations. 
3-6 

Figure 3-5. Number of total DO observations, Dona and Roberts Bays. 

Figure 3-6. Number of total DO observations, Upper Lemon Bay. 
3-7 

Figure 3-7. Number of total DO observations, Lower Lemon Bay. 

Figure 3-8. Number of total DO observations, Tidal Myakka River. 
3-8 

Figure 3-9. Number of total DO observations, Tidal Peace River. 

Figure 3-10. Number of total DO observations, Charlotte Harbor Proper. 
3-9 

Figure 3-11. Number of total DO observations, Pine Island Sound. 

Figure 3-12. Number of total DO observations, Matlacha Pass. 
3-10

Figure 3-13. Number of total DO observations, San Carlos Bay. 

Figure 3-14. Number of total DO observations, Tidal Caloosahatchee River. 
3-11

Figure 3-15. Number of total DO observations, Estero Bay. 
4-1 

4.0 APPROACH 

Descriptive and quantitative analytical techniques were applied in this assessment. The 

data were mapped using ArcGIS (ESRI, 2009) to allow examination of the spatial 

representation of the sampling within the CHNEP area. Spatial and temporal variation 

in DO was investigated using a series of ArcGIS maps and descriptive plots. An 

exploratory data analysis was conducted to investigate the factors affecting dissolved 

oxygen concentrations in the bay segments using logistic regression models to estimate 

the probability of a dissolved oxygen value less than 4 mg/L as a function of potential 

drivers of dissolved oxygen in the segments of the CHNEP area. 
5-1 

5.0 RESULTS 

In this section, the following results are presented: 

 examination of the temporal in DO exceedances in each segment, 

 examination of the spatial patterns in DO in each segment, and

 analysis of the factors affecting the probability of DO exceedances. 

5.1 Temporal Patterns in DO exceedences 

The first step in the analysis was to examine the temporal patterns in DO concentrations 

in each bay segment. Time series plots of all DO measurements are presented in 

Figures 5-1 through 5-11. A different symbol was used for the different sampling 

programs. As expected, the seasonal pattern of lower DO concentrations in the warmer 

summer months and higher DO concentrations in the colder winter months is seen in all 

segments. As discussed in Section 1.0, the FDEP has established the state water 

quality standards (FAC 62.302) to protect the designated uses of Florida waterbodies. 

The state standard for DO is greater than or equal to 4 mg/l in predominantly marine 

waters at all times. The IWR declares a predominantly marine waterbody to be 

impaired if DO is less than 4 mg/L more than 10% of the time (i.e., a 10% exceedance). 

Therefore, a reference line at 4 mg/l is presented on the time series plots to aid the 

reader in identifying measurements that are less than the 4 mg/l. 

In order to determine if the segments are meeting the DO threshold, the annual 

exceedance percentage (i.e., the proportion of the total number of DO samples 

collected within a year that are less than 4 mg/L) for each segment is presented in 

Figures 5-12 through 5-22. The data presented in these figures include all DO samples 

from all programs regardless of sample depth. 

Of the eleven segments, five segments (Upper Lemon Bay, Tidal Myakka, Tidal Peace, 

Matlacha Pass, and Tidal Caloosahatchee) had at least one year in which the 

proportion of DO < 4 mg/l was greater than 10%. The remaining six segments did not 

exhibit any years with a DO exceedence. Of all the segments, San Carlos Bay had the 

lowest percentage of DO exceedences, with the highest annual exceedence percentage 

being only 3%. 

The within-year variation in the percentage of samples less than 4 mg/L for each bay 

segment is shown in Figures 5-23 through 5-33. The influence of temperature and 

salinity on the capacity of estuarine water to hold oxygen is evident. There are very few 

values below 4 mg/L in winter months (November – March), while in summer months 

(June – September) a higher preponderance of observations with a DO value below 4 

mg/L is documented in all segments. As noted in the annual exceedence percentages, 

San Carlos Bay has the lowest percentage of DO exceedences with a maximum 

exceedence of 6.3% in September. 
5-2 

Figure 5-1. Time series of DO concentrations, Dona and Roberts Bays. 

Figure 5-2. Time series of DO concentrations, Upper Lemon Bay. 
5-3 

Figure 5-3. Time series of DO concentrations, Lower Lemon Bay. 

Figure 5-4. Time series of DO concentrations, Tidal Myakka River. 
5-4 

Figure 5-5. Time series of DO concentrations, Tidal Peace River. 

Figure 5-6. Time series of DO concentrations, Charlotte Harbor Proper. 
5-5 

Figure 5-7. Time series of DO concentrations, Pine Island Sound. 

Figure 5-8. Time series of DO concentrations, Matlacha Pass. 
5-6 

Figure 5-9. Time series of DO concentrations, San Carlos Bay. 

Figure 5-10. Time series of DO concentrations, Tidal Caloosahatchee River. 
5-7 

Figure 5-11. Time series of DO concentrations, Estero Bay. 

Figure 5-12. Percent of DO exceedences by year, Dona and Roberts Bays. 
5-8 

Figure 5-13. Percent of DO exceedences by year, Upper Lemon Bay. 

Figure 5-14. Percent of DO exceedences by year, Lower Lemon Bay. 
5-9 

Figure 5-15. Percent of DO exceedences by year, Tidal Myakka River. 

Figure 5-16. Percent of DO exceedences by year, Tidal Peace River. 
5-10

Figure 5-17. Percent of DO exceedences by year, Charlotte Harbor Proper. 

Figure 5-18. Percent of DO exceedences by year, Pine Island Sound. 
5-11

Figure 5-19. Percent of DO exceedences by year, Matlacha Pass. 

Figure 5-20. Percent of DO exceedences by year, San Carlos Bay. 
5-12

Figure 5-21. Percent of DO exceedences by year, Tidal Caloosahatchee River. 

Figure 5-22. Percent of DO exceedences by year, Estero Bay. 
5-13

Figure 5-23. Percent of DO exceedences by calendar month, Dona and Roberts Bays. 

Figure 5-24. Percent of DO exceedences by calendar month, Upper Lemon Bay. 
5-14

Figure 5-25. Percent of DO exceedences by calendar month, Lower Lemon Bay. 

Figure 5-26. Percent of DO exceedences by calendar month, Tidal Myakka River. 
5-15

Figure 5-27. Percent of DO exceedences by calendar month, Tidal Peace River. 

Figure 5-28. Percent of DO exceedences by calendar month, Charlotte Harbor Proper. 
5-16

Figure 5-29. Percent of DO exceedences by calendar month, Pine Island Sound. 

Figure 5-30. Percent of DO exceedences by calendar month, Matlacha Pass. 
5-17

Figure 5-31. Percent of DO exceedences by calendar month, San Carlos Bay. 

Figure 5-32. Percent of DO exceedences by calendar month, Tidal Caloosahatchee River. 
5-18

Figure 5-33. Percent of DO exceedences by calendar month, Estero Bay. 

5.2 Spatial Patterns in DO exceedences 

In order to better understand the spatial variation in DO among segments, a box and 

whisker plot of DO measurements by segment is presented in Figure 5-34. The box 

represents the interquartile range (25th, 50th [median], and 75th percentiles), while the 

whiskers represent the minimum and maximum DO measurements. The average DO 

for the segment is represented by the blue dot. The average DO ranged from 6.1 mg/l 

in Dona and Roberts Bays to 7.3 mg/l in Pine Island Sound. Variability was somewhat 

lower in the northern segments (Dona and Roberts Bays, Upper Lemon Bay, and Lower 

Lemon Bay) where the lowest DO concentration was 1.96 mg/l and the highest DO 

concentration was 12 mg/l. The greatest variability was seen in Charlotte Harbor 

Proper (0.05 – 18.3 mg/l) and Pine Island Sound (0.5 – 17.8 mg/l). The 25th percentile 

DO concentrations ranged from 5.2 mg/l (Estero Bay) to 6.2 mg/l (Pine Island Sound), 

meaning that at least 75% of the DO measurements were greater than 5.2 mg/l in all 

segments. 
5-19

Figure 5-34. Distribution of DO values in each of the CHNEP segments. 

To identify areas with a higher potential for DO exceedences, the spatial distribution of 

DO values throughout each segment was investigated during the warmest months of 

the year when low DO values are most likely to occur (Figures 5-23 through 5-33). All 

data collected from June through September were mapped in ArcGIS for the Upper 

portion of the CHNEP area (Figure 5-35 including Dona and Roberts Bays, Upper 

Lemon Bay, and Lower Lemon Bay), northern rivers and Charlotte Harbor (Figure 5-36 

including the Tidal Myakka River, Tidal Peace River, and Charlotte Harbor Proper), and 

lower Charlotte Harbor (Figure 5-37 including Pine Island Sound, Matlacha Pass, San 

Carlos Bay, Tidal Caloosahatchee River, and Estero Bay). The sampling points were 

labeled using a graduated scale from 0 to 4 by 1.0 mg/L increments and those over 4 

mg/L were labeled as a single color (blue). When sample points fell on top of one 

another the lowest value was displayed to denote the lowest value recorded in that 

area. Therefore, it is important to note that this map does not represent typical 

conditions but rather is meant to highlight areas that may be susceptible to a low DO 

occurrence under certain circumstances. These circumstances are further investigated 

later in this document. 
5-20

Figure 5-35. Spatial distribution of DO during summer months (June-September) for the 

northern portion of the CHNEP area. 
5-21

Figure 5-36. Spatial distribution of DO during summer months (June-September) for Tidal 

Myakka, Tidal Peace, and Charlotte Harbor Proper. 

A summary of DO measurements by segment for the months of June through 

September is presented in Table 5-1. As with the maps, the data in the table represent 

the percentage of DO observations during the June through September period for 

different DO ranges (0-1 mg/l, 1-2 mg/l, 2-3 mg/l, 3-4 mg/l, and > 4mg/l). The majority 

of DO measurements less than 2 mg/l occurred in the Tidal Peace River and Charlotte 

Harbor Proper. Even though these data represent the season that typically has the 

lowest DO concentrations, three segments (Lower Lemon Bay, Matlacha Pass, and San 

Carlos Bay) have greater than 90% of the DO measurements greater than 4 mg/l. With 

the exception of Tidal Peace River and Charlotte Harbor Proper, the majority of the 

observations less than 4 mg/l during the June through September period were in the 3-4 

mg/l range. 
5-22

Figure 5-37. Spatial distribution of DO during summer months (June-September) for the 

southern portion of the CHNEP area. 

Table 5-1. Summary of DO observations by segment for the months June through 

September.

Bay Segment

# of 

Observations

% of observations:

0-1 mg/l 1-2 mg/l 2-3 mg/l 3-4 mg/l >4 mg/l

Dona and Roberts Bays 123 0.0% 0.0% 4.1% 9.8% 86.2%

Upper Lemon Bay 225 0.0% 0.4% 4.4% 12.0% 83.1%

Lower Lemon Bay 167 0.0% 0.0% 0.0% 9.6% 90.4%

Tidal Myakka 1541 0.3% 0.6% 2.7% 10.8% 85.7%

Tidal Peace 2423 2.5% 2.7% 4.9% 12.8% 77.1%

Charlotte Harbor Proper 3978 1.6% 2.3% 3.5% 7.2% 85.4%

Matlacha Pass 2519 0.2% 1.1% 2.4% 5.6% 90.7%

Pine Island Sound 1211 0.4% 1.5% 4.5% 10.9% 82.7%

San Carlos Bay 1237 0.2% 0.1% 0.9% 3.6% 95.2%

Tidal Caloosahatchee 1676 0.2% 0.8% 3.2% 11.2% 84.7%

Estero Bay 1094 0.6% 0.4% 1.3% 7.9% 89.9%
5-23

Examination of these maps and data indicates the following: 

 While DO concentrations less than 4 mg/l are found throughout the CHNEP area, 

the majority of DO concentrations less than 2 mg/l were in the Tidal Peace River 

and Charlotte Harbor Proper. 

 The northern segments (Dona and Roberts Bays, Upper Lemon Bay, and Lower 

Lemon Bay) have fewer DO values less than 2 mg/l than other segments and 

have less variability 

 For all segments except the Tidal Peace River and Charlotte Harbor Proper, the 

majority of the observations less than 4 mg/l during the June through September 

period were in the 3-4 mg/l range. 

5.3 Factors Affecting DO Exceedences 

As discussed in Section 1.0, the conceptual model applied by FDEP in establishing the 

DO standard is that excess nutrients from anthropogenic sources result in algal blooms 

which in turn result in increased organic deposition and decomposition which in turn 

lead to reduced DO concentrations. Symptoms of eutrophication include excess 

primary production, deposition and decomposition of phytodetritus and consequently 

increased biological oxygen demand which reduces the DO content of estuarine waters 

(Nixon, 1995). The objective of this effort was to assess the percentage of state 

standard exceedances in DO and assess drivers of DO exceedances in the segments 

of the CHNEP area with respect to the development of recently proposed numeric 

nutrient criteria for the Sarasota Bay estuary (Janicki Environmental, 2011a; 2011b).

In order to better understand the factors that influence DO, a series of regressions were 

developed. 

A preliminary ordinary least squares regression analysis of DO and potential 

explanatory variables revealed that an increase in temperature was the main driver of 

lower DO concentrations (Pr > F <0.0001, r2 = 0.32) for the CHNEP area. While this 

information is useful, further analysis was required to better understand what influences 

the probability of DO concentrations less than 4 mg/l in individual segments. To this 

end, a series of stepwise logistic regressions were developed for individual segments to 

identify the variables that influence the probability of a DO concentration less than 4 

mg/l. 

The parameter estimates, resulting odds ratio estimates, chi-square values, and 

Hosmer & Lemeshow Goodness-of-Fit Test output are provided in Table 5-2. The 

relative effect of individual parameter estimates on the change in probability of 

observing a DO < 4 mg/L can be assessed using either the odds ratio estimate or the 

chi-square values associated with the significance test. An odds ratio of 1 is equivalent 

to a rate of change of 0 and indicates a variable has little influence on the predicted 

probability. For example, for Dona and Roberts Bays the odds ratio for temperature is 

1.312. Therefore, for a one unit increase in temperature, there is a 31% increase in the 

probability of a DO concentration less than 4 mg/l occurring. 
5-24

In all segments, temperature is the primary factor that is positively correlated with a DO 

exceedence (a DO concentration < 4 mg/l). Though chlorophyll is included in the 

models of three segments (Tidal Myakka, Pine Island Sound, and Tidal 

Caloosahatchee), in Tidal Myakka and Tidal Caloosahatchee an increase in chlorophyll 

leads to a decrease in the probability of a DO exceedence. This contradicts the 

conceptual model proposed by FDEP and discussed in Section 1.0. Output from the 

Hosmer & Lemeshow Goodness-of-Fit Test is used to assess the fit of the models. As 

can be seen in the table, there is no evidence of a lack of fit in the models except for 

Upper Lemon Bay, Tidal Peace River, and Charlotte Harbor Proper. 

Table 5-2. Logistic regression parameter estimates including odds ratios, 

significance levels, and overall model goodness-of-fit (Hosmer and 

Lemeshow). The response variable is the probability of a bottom DO < 4 

mg/l.

Bay Segment (Hosmer 

& Lemeshow 

Goodness-of-Fit Test) Parameter Coefficient

Odds 

Ratio

ChisquarePr > Chisquare

Dona and Roberts Bays 

(Pr > ChiSq 0.86)

Color 0.1047 1.009 45.5 <0.0001

Temperature 0.2062 1.312 14.1 0.0002

Upper Lemon Bay

(Pr > ChiSq 0.01)

Color 0.0116 1.012 43.4 <0.0001

Temperature 0.1347 1.144 24.6 <0.0001

Lower Lemon Bay

(Pr > ChiSq 0.06)

Color 0.0262 1.027 41.1 <0.0001

Temperature 0.0860 1.090 12.9 0.0003

Tidal Myakka

(Pr > ChiSq 0.22)

Color 0.0112 1.011 225.9 <0.0001

Temperature 0.5840 1.793 29.6 <0.0001

Chlorophyll -0.2083 0.812 15.7 <0.0001

Tidal Peace

(Pr > ChiSq 0.004)

Temperature 0.2398 1.192 88.5 <0.0001

Color 0.0043 1.004 21.6 <0.0001

Charlotte Harbor Proper 

(Pr > ChiSq 0.05)

Temperature 0.1376 1.148 62.8 <0.0001

Color 0.0064 1.004 21.6 <0.0001

Matlacha Pass

(Pr > ChiSq 0.54) Temperature 0.2058 1.228 31.7 <0.0001

Pine Island Sound

(Pr > ChiSq 0.62)

Chlorophyll 0.0520 1.053 9.7 0.0019

Temperature 0.0907 1.095 3.7 0.0537

San Carlos Bay 

(Pr > ChiSq 0.43)

Temperature 0.1822 1.200 15.4 <0.0001

Color -0.0126 0.987 2.9 0.0866

Tidal Caloosahatchee

(Pr > ChiSq 0.29)

Color 0.0133 1.013 115.9 <0.0001

Temperature 0.2479 1.281 20.4 <0.0001

Chlorophyll -0.0591 0.943 8.1 0.0045

Estero Bay

(Pr > ChiSq 0.16)

Temperature 0.1468 1.158 46.0 <0.0001

Color 0.0125 1.013 17.5 <0.0001
5-25

As was discussed in Section 2.0, Camp, Dresser, and McKee (1998) found that salinity 

stratification was prevalent during periods of low DO concentrations in the Tidal Peace 

River and Charlotte Harbor. Salinity stratification is known to result in depressed 

dissolved oxygen layers as a freshwater lens builds on surface waters restricting the 

exchange of bottom water with the atmosphere. To investigate the degree to which 

salinity stratification occurs in the CHNEP area, the difference between bottom and 

surface salinity was calculated from every observation where both surface and bottom 

values were recorded (generally where depths were greater than 1 meter). The data 

are summarized in Table 5-3. Statistics could not be calculated for Dona and Roberts 

Bays and Upper Lemon Bay as only surface samples were reported. As expected, the 

degree of stratification varies widely in the CHNEP area as some segments have major 

freshwater inflows and others have relatively little freshwater inflow. The segments with 

the largest freshwater inflows (Tidal Peace, Tidal Caloosahatchee, and San Carlos Bay) 

had the greatest stratification while Lower Lemon Bay and Pine Island Sound had the 

least stratification. 

Table 5-3. Summary statistics of stratification (bottom salinity – surface salinity) by 

segment.

Bay Segment 50th

Percentile

75th

Percentile

90th

Percentile

95th

Percentile

99th

Percentile

Dona and Roberts Bays n/a n/a n/a n/a n/a

Upper Lemon Bay n/a n/a n/a n/a n/a

Lower Lemon Bay 0.0 0.1 0.2 0.4 2.0

Tidal Myakka 0.0 0.3 1.6 3.1 6.6

Tidal Peace 0.2 2.2 7.1 10.1 16.3

Charlotte Harbor Proper 0.0 0.3 1.9 4.2 10.8

Matlacha Pass 0.0 0.1 1.1 3.4 9.0

Pine Island Sound 0.0 0.1 0.7 2.0 5.7

Tidal Caloosahatchee 0.0 1.0 3.7 5.8 11.7

San Carlos Bay 0.2 1.4 6.1 8.8 14.5

Estero Bay 0.0 0.3 2.1 5.0 8.8

There was evidence of a lack of fit in the models developed for several of the segments, 

therefore, additional models were developed. These models estimate the probability of 

a bottom DO less than 4 mg/l as a function of several explanatory variables, including 

salinity stratification. The parameter estimates, resulting odds ratio estimates, chisquare values, and Hosmer & Lemeshow Goodness-of-Fit Test output are provided in 

Table 5-4 for Charlotte Harbor Proper and Tidal Peace River (Upper Lemon Bay was 

not included because of a lack of salinity stratification data). There was no evidence of 

a lack of fit in the models. Temperature and stratification were the main drivers of DO 

exceedences in these two segments. Chlorophyll was not a significant predictor of 

bottom DO exceedences in either of the models. 
5-26

Table 5-4. Summary of DO observations by segment for the months June through 

September.

Bay Segment (Hosmer 

& Lemeshow 

Goodness-of-Fit Test) Parameter Coefficient

Odds 

Ratio

ChisquarePr > Chisquare

Tidal Peace

(Pr > ChiSq 0.84)

Temperature 0.4888 1.630 92.1 <0.0001

Stratification 0.1996 1.221 30.9 <0.0001

Color 0.0034 1.003 4.0 0.0451

Charlotte Harbor Proper

(Pr > ChiSq 0.79)

Stratification 0.4448 1.560 102.2 <0.0001

Temperature 0.5643 1.758 46.9 <0.0001

Color 0.0160 0.999 3.6 0.0573
6-1 

6.0 CONCLUSIONS 

The following conclusions can be drawn from the analyses presented above: 

 The empirical evidence presented above suggests that the majority of CHNEP 

segments are meeting full aquatic life uses with respect to DO. Six segments 

(Dona and Roberts Bays, Lower Lemon Bay, Charlotte Harbor Proper, Pine 

Island Sound, San Carlos Bay, and Estero Bay) had no annual DO exceedences. 

Of the five segments that had exceedences, Tidal Myakka and Tidal 

Caloosahatchee had a single exceedence while Upper Lemon Bay, Tidal Peace, 

and Matlacha Pass had three exceedences each. Examination of spatial 

distribution revealed no strong tendencies for DO less than 4 mg/l. However, the 

probability of DO values less than 2 mg/l was highest in the Tidal Peace and the 

upper portion of Charlotte Harbor Proper. Previous work by Camp, Dresser & 

McKee (1998) revealed that stratification was more prevalent when low DO 

concentrations occurred in the Tidal Peace and Charlotte Harbor. Logistic 

regression models developed for this report confirm that stratification is one of 

the principle drivers of DO exceedences in the Tidal Peace and Charlotte Harbor. 

 The principal factor affecting DO in the segments of the CHNEP is temperature. 

This fact is evident in both the descriptive time-series plots and the results of 

ordinary least-squares regression. 

 Additional models were developed to identify the explanatory variables that 

contribute to the probability of DO exceedences at the segment level. In all 

segments, temperature is the primary factor that is positively associated with a 

DO exceedence (a DO concentration < 4 mg/l). Though chlorophyll is included in 

the models of three segments (Tidal Myakka, Pine Island Sound, and Tidal 

Caloosahatchee), in Tidal Myakka and Tidal Caloosahatchee an increase in 

chlorophyll leads to a decrease in the probability of a DO exceedence. This 

contradicts the conceptual model proposed by FDEP that excess nutrients from 

anthropogenic assaults result in algal blooms which result in increased organic 

deposition and decomposition which in turn lead to reduced DO concentrations. 

 There was evidence of a lack of fit in the models developed for several of the 

segments, therefore additional models were developed for these segments. 

These models estimate the probability of a bottom DO less than 4 mg/l as a 

function of several explanatory variables, including salinity stratification. There 

was no evidence of a lack of fit in the additional models. Temperature and 

stratification were the main drivers of DO exceedences in Tidal Peace and 

Charlotte Harbor Proper. Chlorophyll was not a significant predictor of bottom 

DO exceedences in either of the segments. 

 Based on the weight-of-evidence presented here, it is reasonable to conclude 

that the proposed numeric nutrient criteria, which are based on a reference 

period approach, are protective of full aquatic life uses with respect to DO. 
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Hypoxia in Upper Charlotte Harbor. 

Duffey, R., R. E. Leary, and J. Ott. 2007. Charlotte Harbor and Estero Bay Aquatic 

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Charlotte Harbor National Estuary Program. 

Environmental Systems Research Institute (ESRI), Inc. 2009. ArcGIS Version 9.2. 

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

Estuarine Waters of the Charlotte Harbor National Estuary Program, Task 7: Numeric 

Nutrient Criteria Development, Interim Report 6. Prepared for: Charlotte Harbor 

National Estuary Program. 

Janicki Environmental, Inc. 2011b. Charlotte Harbor Numeric Nutrient Criteria: Task 8 - 

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