Funding & Acknowledgements

The data used in this analysis is from the Export Standardized Tables in the SEACAR Data Discovery Interface (DDI). Documents and information available through the SEACAR DDI are owned by the data provider(s) and users are expected to provide appropriate credit following accepted citation formats. Users are encouraged to access data to maximize utilization of gained knowledge, reducing redundant research and facilitating partnerships and scientific innovation.

With respect to documents and information available from SEACAR DDI, neither the State of Florida nor the Florida Department of Environmental Protection makes any warranty, expressed or implied, including the warranties of merchantability and fitness for a particular purpose arising out of the use or inability to use the data, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

This report was funded in part, through a grant agreement from the Florida Department of Environmental Protection, Florida Coastal Management Program, by a grant provided by the Office for Coastal Management under the Coastal Zone Management Act of 1972, as amended, National Oceanic and Atmospheric Administration. The views, statements, findings, conclusions and recommendations expressed herein are those of the author(s) and do not necessarily reflect the views of the State of Florida, NOAA or any of their sub agencies.

Published: 2025-10-08

Threshold Filtering

Threshold filters, following the guidance of Florida Department of Environmental Protection’s (FDEP) Division of Environmental Assessment and Restoration (DEAR) are used to exclude specific results values from the SEACAR Analysis. Based on the threshold filters, Quality Assurance / Quality Control (QAQC) Flags are inserted into the SEACAR_QAQCFlagCode and SEACAR_QAQC_Description columns of the export data. The Include column indicates whether the QAQC Flag will also indicate that data are excluded from analysis. No data are excluded from the data export, but the analysis scripts can use the Include column to exclude data (1 to include, 0 to exclude).

Continuous Water Quality threshold values
Parameter Name Units Low Threshold High Threshold
Dissolved Oxygen mg/L -0.000001 50
Dissolved Oxygen Saturation % -0.000001 500
Salinity ppt -0.000001 70
Turbidity NTU -0.000001 4000
Water Temperature Degrees C -5.000000 45
pH None 2.000000 14
Discrete Water Quality threshold values
Parameter Name Units Low Threshold High Threshold
Ammonia, Un-ionized (NH3) mg/L - -
Ammonium, Filtered (NH4) mg/L - -
Chlorophyll a, Corrected for Pheophytin ug/L - -
Chlorophyll a, Uncorrected for Pheophytin ug/L - -
Colored Dissolved Organic Matter PCU - -
Dissolved Oxygen mg/L -0.000001 25
Dissolved Oxygen Saturation % -0.000001 310
Fluorescent Dissolved Organic Matter QSE - -
Light Extinction Coefficient m^-1 - -
NO2+3, Filtered mg/L - -
Nitrate (NO3) mg/L - -
Nitrite (NO2) mg/L - -
Nitrogen, organic mg/L - -
Phosphate, Filtered (PO4) mg/L - -
Salinity ppt -0.000001 70
Secchi Depth m 0.000001 50
Specific Conductivity mS/cm 0.005000 100
Total Kjeldahl Nitrogen mg/L - -
Total Nitrogen mg/L - -
Total Nitrogen mg/L - -
Total Phosphorus mg/L - -
Total Suspended Solids mg/L - -
Turbidity NTU - -
Water Temperature Degrees C 3.000000 40
pH None 2.000000 13
Quality Assurance Flags inserted based on threshold checks listed in Table 1 and 2
SEACAR QAQC Description Include SEACAR QAQCFlagCode
Exceeds maximum threshold 0 2Q
Below minimum threshold 0 4Q
Within threshold tolerance 1 6Q
No defined thresholds for this parameter 1 7Q

Value Qualifiers

Value qualifier codes included within the data are used to exclude certain results from the analysis. The data are retained in the data export files, but the analysis uses the Include column to filter the results.

STORET and WIN value qualifier codes

Value qualifier codes from STORET and WIN data are examined with the database and used to populate the Include column in data exports.

Value Qualifier codes excluded from analysis
Qualifier Source Value Qualifier Include MDL Description
STORET-WIN H 0 0 Value based on field kit determination; results may not be accurate
STORET-WIN J 0 0 Estimated value
STORET-WIN V 0 0 Analyte was detected at or above method detection limit
STORET-WIN Y 0 0 Lab analysis from an improperly preserved sample; data may be inaccurate

Discrete Water Quality Value Qualifiers

The following value qualifiers are highlighted in the Discrete Water Quality section of this report. An exception is made for Program 476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network and data flagged with Value Qualifier H are included for this program only.

H - Value based on field kit determiniation; results may not be accurate. This code shall be used if a field screening test (e.g., field gas chromatograph data, immunoassay, or vendor-supplied field kit) was used to generate the value and the field kit or method has not been recognized by the Department as equivalent to laboratory methods.

I - The reported value is greater than or equal to the laboratory method detection limit but less than the laboratory practical quantitation limit.

Q - Sample held beyond the accepted holding time. This code shall be used if the value is derived from a sample that was prepared or analyzed after the approved holding time restrictions for sample preparation or analysis.

S - Secchi disk visible to bottom of waterbody. The value reported is the depth of the waterbody at the location of the Secchi disk measurement.

U - Indicates that the compound was analyzed for but not detected. This symbol shall be used to indicate that the specified component was not detected. The value associated with the qualifier shall be the laboratory method detection limit. Unless requested by the client, less than the method detection limit values shall not be reported

Systemwide Monitoring Program (SWMP) value qualifier codes

Value qualifier codes from the SWMP continuous program are examined with the database and used to populate the Include column in data exports. SWMP Qualifier Codes are indicated by QualifierSource=SWMP.

SWMP Value Qualifier codes
Qualifier Source Value Qualifier Include Description
SWMP -1 1 Optional parameter not collected
SWMP -2 0 Missing data
SWMP -3 0 Data rejected due to QA/QC
SWMP -4 0 Outside low sensor range
SWMP -5 0 Outside high sensor range
SWMP 0 1 Passed initial QA/QC checks
SWMP 1 0 Suspect data
SWMP 2 1 Reserved for future use
SWMP 3 1 Calculated data: non-vented depth/level sensorcorrection for changes in barometric pressure
SWMP 4 1 Historical: Pre-auto QA/QC
SWMP 5 1 Corrected data

Water Column

The water column habitat extends from the water’s surface to the bottom sediments, and it’s where fish, dolphins, crabs and people swim! So much life makes its home in the water column that the health of marine and coastal ecosystems, as well as human economies, depend on the condition of this vulnerable habitat. Local patterns of rainfall, temperature, winds and currents can rapidly change the condition of the water column, while global influences such as El Niño/La Niña, large-scale fluctuation in sea temperatures and climate change can have long-term effects. Inputs from the prosperity of our day-to-day lives including farming, mining and forestry, and emissions from power generation, automobiles and water treatment can also alter the health of the water column. Acting alone or together, each input can have complex and lasting effects on habitats and ecosystems.


SEACAR evaluates water column health with several essential parameters. These include nutrient surveys of nitrogen and phosphorus, and water quality assessments of salinity, dissolved oxygen, pH, and water temperature. Water clarity is evaluated with Secchi depth, turbidity, levels of chlorophyll a, total suspended solids, and colored dissolved organic matter. Additionally, the richness of nekton is indicated by the abundance of free-swimming fishes and macroinvertebrates like crabs and shrimps.

Seasonal Kendall-Tau Analysis

Indicators must have a minimum of five to ten years, depending on the habitat, of data within the geographic range of the analysis to be included in the analysis. Ten years of data are required for discrete parameters, and five years of data are required for continuous parameters. If there are insufficient years of data, the number of years of data available will be noted and labeled as “insufficient data to conduct analysis”. Further, for the preferred Seasonal Kendall-Tau test, there must be data from at least two months in common across at least two consecutive years within the RCP managed area being analyzed. Values that pass both of these tests will be included in the analysis and be labeled as Use_In_Analysis = TRUE. Any that fail either test will be excluded from the analyses and labeled as Use_In_Analysis = FALSE. The points for all Water Column plots displayed in this section are monthly averages. Trend significance will be denoted as “Significant Trend” (when p < 0.05), or “Non-significant Trend” (when p >= 0.05). Any parameters with insufficient data to perform Seasonal Kendall-Tau test will have their monthly averages plotted without a corresponding trend line.

Water Quality - Discrete

The following files were used in the discrete analysis:

  • Combined_WQ_WC_NUT_Chlorophyll_a_corrected_for_pheophytin-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Chlorophyll_a_uncorrected_for_pheophytin-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Colored_dissolved_organic_matter_CDOM-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Dissolved_Oxygen-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Dissolved_Oxygen_Saturation-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_pH-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Salinity-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Secchi_Depth-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Total_Nitrogen-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Total_Phosphorus-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Total_Suspended_Solids_TSS-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Turbidity-2025-Sep-04.txt

  • Combined_WQ_WC_NUT_Water_Temperature-2025-Sep-04.txt

Chlorophyll a, Corrected for Pheophytin - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average levels of chlorophyll a, corrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Scatter plot of monthly average levels of chlorophyll a, corrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Seasonal Kendall-Tau Trend Analysis for Chlorophyll a, Corrected for Pheophytin
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab Significantly decreasing trend 1068 23 1998 - 2025 4.7 -0.1635 6.6163 -0.0838 0.0004

Monthly average chlorophyll a, corrected for pheophytin, decreased by 0.08 µg/L per year, indicating an increase in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Chlorophyll a, Corrected for Pheophytin
ProgramID N_Data YearMin YearMax
476 725 2008 2025
5002 370 1998 2024

Program names:

476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
5002 - Florida STORET / WIN2

Chlorophyll a, Uncorrected for Pheophytin - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average levels of chlorophyll a, uncorrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Scatter plot of monthly average levels of chlorophyll a, uncorrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Seasonal Kendall-Tau Trend Analysis for Chlorophyll a, Uncorrected for Pheophytin
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab No significant trend 781 20 1998 - 2025 4.01 -0.085 4.8191 -0.0395 0.1577

Chlorophyll a, uncorrected for pheophytin, showed no detectable trend between 1998 and 2025.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Chlorophyll a, Uncorrected for Pheophytin
ProgramID N_Data YearMin YearMax
476 626 1998 2025
5002 178 2017 2023
95 13 2003 2013
103 2 2005 2005
118 1 2005 2005

Program names:

95 - Harmful Algal Bloom Marine Observation Network3
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
5002 - Florida STORET / WIN2

Dissolved Oxygen - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average dissolved oxygen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen values measured in the field (circles) are included in the plot.
Scatter plot of monthly average dissolved oxygen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen values measured in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Dissolved Oxygen
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field No significant trend 13265 38 1971 - 2025 6.1 -0.0573 6.3118 -0.0074 0.0907

Dissolved oxygen showed no detectable trend between 1971 and 2025.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Dissolved Oxygen
ProgramID N_Data YearMin YearMax
5002 9922 1995 2025
476 1036 1998 2025
69 924 1989 2024
479 865 2001 2016
95 647 1971 2018
118 5 2005 2020

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program6
95 - Harmful Algal Bloom Marine Observation Network3
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
479 - Southwest Florida Water Management District - Water Quality Monitoring7
5002 - Florida STORET / WIN2

Dissolved Oxygen Saturation - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average dissolved oxygen saturation over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen saturation values measured in the field (circles) are included in the plot.
Scatter plot of monthly average dissolved oxygen saturation over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen saturation values measured in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Dissolved Oxygen Saturation
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly decreasing trend 4623 28 1998 - 2025 87 -0.1017 87.0974 -0.1928 0.0117

Monthly average dissolved oxygen saturation decreased by 0.19% per year.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Dissolved Oxygen Saturation
ProgramID N_Data YearMin YearMax
5002 4436 1998 2025
476 233 2018 2025
95 4 2005 2018

Program names:

95 - Harmful Algal Bloom Marine Observation Network3
476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
5002 - Florida STORET / WIN2

pH - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average pH over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only pH values measured in the field (circles) are included in the plot.
Scatter plot of monthly average pH over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only pH values measured in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for pH
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly decreasing trend 11689 38 1955 - 2025 8 -0.094 8.0867 -0.002 0.0077

Monthly average pH decreased by less than 0.01 pH units per year.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for pH
ProgramID N_Data YearMin YearMax
5002 8308 1995 2025
476 1051 1998 2025
69 922 1989 2024
479 869 2001 2016
95 625 1955 2018

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program6
95 - Harmful Algal Bloom Marine Observation Network3
476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
479 - Southwest Florida Water Management District - Water Quality Monitoring7
5002 - Florida STORET / WIN2

Salinity - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average salinity over time. If the time series included ten or more years of discrete observations, significant (blue) or non-significant (magenta) trend lines are also shown. Discrete salinity values derived from grab samples analyzed in the field (circles) or the laboratory (triangles) are both included in the plot.
Scatter plot of monthly average salinity over time. If the time series included ten or more years of discrete observations, significant (blue) or non-significant (magenta) trend lines are also shown. Discrete salinity values derived from grab samples analyzed in the field (circles) or the laboratory (triangles) are both included in the plot.
Seasonal Kendall-Tau Trend Analysis for Salinity
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
All Significantly decreasing trend 11361 58 1954 - 2025 34 -0.0992 34.7975 -0.0181 0.001

Monthly average salinity decreased by 0.02 ppt per year.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Salinity
ProgramID N_Data YearMin YearMax
5002 6583 1995 2025
95 1521 1954 2018
476 1060 1998 2025
69 935 1989 2024
479 870 2001 2016
513 407 2001 2009
118 4 2020 2020

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program6
95 - Harmful Algal Bloom Marine Observation Network3
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
479 - Southwest Florida Water Management District - Water Quality Monitoring7
513 - Coastal Charlotte Harbor Monitoring Network8
5002 - Florida STORET / WIN2

Secchi Depth - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average Secchi depth over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Secchi depth is only measured in the field (circles).
Scatter plot of monthly average Secchi depth over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Secchi depth is only measured in the field (circles).
Seasonal Kendall-Tau Trend Analysis for Secchi Depth
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly decreasing trend 3083 31 1995 - 2025 -1.3 -0.2871 -1.0356 -0.0167 0

Monthly average Secchi depth became deeper by 0.02 m per year, indicating an increase in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Secchi Depth
ProgramID N_Data YearMin YearMax
5002 922 2007 2025
69 892 1995 2024
476 812 1998 2025
479 445 2001 2016
103 14 1995 2020

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program6
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
479 - Southwest Florida Water Management District - Water Quality Monitoring7
5002 - Florida STORET / WIN2

Total Nitrogen - Discrete

Total Nitrogen Calculation:

The logic for calculated Total Nitrogen was provided by Kevin O’Donnell and colleagues at FDEP (with the help of Jay Silvanima, Watershed Monitoring Section). The following logic is used, in this order, based on the availability of specific nitrogen components.

  1. TN = TKN + NO3O2;
  2. TN = TKN + NO3 + NO2;
  3. TN = ORGN + NH4 + NO3O2;
  4. TN = ORGN + NH4 + NO2 + NO3;
  5. TN = TKN + NO3;
  6. TN = ORGN + NH4 + NO3;

Additional Information:

  • Rules for use of sample fraction:
    • Florida Department of Environmental Protection (FDEP) report that if both “Total” and “Dissolved” components are reported, only “Total” is used. If the total is not reported, then the dissolved components are used as a best available replacement.
    • Total nitrogen calculations are done using nitrogen components with the same sample fraction, nitrogen components with mixed total/dissolved sample fractions are not used. In other words, total nitrogen can be calculated when TKN and NO3O2 are both total sample fractions, or when both are dissolved sample fractions. Future calculations of total nitrogen values may be based on components with mixed sample fractions.
  • Values inserted into data:
    • ParameterName = “Total Nitrogen”
    • SEACAR_QAQCFlagCode = “1Q”
    • SEACAR_QAQC_Description = “SEACAR Calculated”

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average total nitrogen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only nitrogen values obtained from laboratory analyses (triangles) are included in the plot.
Scatter plot of monthly average total nitrogen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only nitrogen values obtained from laboratory analyses (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Total Nitrogen
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab No significant trend 2889 30 1995 - 2025 0.557 0.0449 0.5454 0.001 0.2389

Total nitrogen showed no detectable trend between 1995 and 2025.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Total Nitrogen
ProgramID N_Data YearMin YearMax
5002 1766 1995 2025
476 967 1998 2025
479 152 2007 2016
103 4 2005 2005

Program names:

103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
479 - Southwest Florida Water Management District - Water Quality Monitoring7
5002 - Florida STORET / WIN2

Total Phosphorus - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average total phosphorus over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only phosphorus values obtained from laboratory analyses (triangles) are included in the plot.
Scatter plot of monthly average total phosphorus over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only phosphorus values obtained from laboratory analyses (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Total Phosphorus
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab Significantly decreasing trend 2944 30 1995 - 2025 0.09 -0.5378 0.184 -0.005 0

Monthly average total phosphorus decreased by less than 0.01 mg/L per year.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Total Phosphorus
ProgramID N_Data YearMin YearMax
5002 1773 1995 2025
476 1079 1998 2025
479 152 2007 2016
103 4 2005 2005

Program names:

103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
479 - Southwest Florida Water Management District - Water Quality Monitoring7
5002 - Florida STORET / WIN2

Total Suspended Solids - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average total suspended solids (TSS) over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only TSS values obtained from laboratory analyses (triangles) are included in the plot.
Scatter plot of monthly average total suspended solids (TSS) over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only TSS values obtained from laboratory analyses (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Total Suspended Solids
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab Significantly increasing trend 1068 28 1995 - 2024 10.5 0.3245 3.4879 0.4081 0

Monthly average total suspended solids increased by 0.41 mg/L per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Total Suspended Solids
ProgramID N_Data YearMin YearMax
5002 917 1995 2024
513 172 2001 2009
479 152 2007 2016

Program names:

479 - Southwest Florida Water Management District - Water Quality Monitoring7
513 - Coastal Charlotte Harbor Monitoring Network8
5002 - Florida STORET / WIN2

Turbidity - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average turbidity over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only turbidity values measured in the laboratory (triangles) are included in the plot.
Scatter plot of monthly average turbidity over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only turbidity values measured in the laboratory (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Turbidity
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab No significant trend 5961 31 1995 - 2025 2.6 0.0699 2.8844 0.0141 0.0613

Turbidity showed no detectable trend between 1995 and 2025.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Turbidity
ProgramID N_Data YearMin YearMax
5002 4665 1995 2025
476 1118 1998 2025
479 278 2001 2016
513 185 2001 2009
95 14 2003 2004
103 2 2005 2005

Program names:

95 - Harmful Algal Bloom Marine Observation Network3
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
479 - Southwest Florida Water Management District - Water Quality Monitoring7
513 - Coastal Charlotte Harbor Monitoring Network8
5002 - Florida STORET / WIN2

Water Temperature - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average water temperature over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only water temperature measurements taken in the field (circles) are included in the plot.
Scatter plot of monthly average water temperature over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only water temperature measurements taken in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Water Temperature
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly increasing trend 14451 59 1954 - 2025 26.4 0.1201 24.5279 0.0149 0.0001

Monthly average water temperature increased by 0.01°C per year.

Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Water Temperature
ProgramID N_Data YearMin YearMax
5002 10263 1995 2025
95 1330 1954 2018
476 1067 1998 2025
69 940 1989 2024
479 865 2001 2016

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program6
95 - Harmful Algal Bloom Marine Observation Network3
476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network1
479 - Southwest Florida Water Management District - Water Quality Monitoring7
5002 - Florida STORET / WIN2

Submerged Aquatic Vegetation

The data file used is: All_SAV_Parameters-2025-Sep-04.txt

Submerged aquatic vegetation (SAV) refers to plants and plant-like macroalgae species that live entirely underwater. The two primary categories of SAV inhabiting Florida estuaries are benthic macroalgae and seagrasses. They often grow together in dense beds or meadows that carpet the seafloor. Macroalgae include multicellular species of green, red and brown algae that often live attached to the substrate by a holdfast. They tend to grow quickly and can tolerate relatively high nutrient levels, making them a threat to seagrasses and other benthic habitats in areas with poor water quality. In contrast, seagrasses are grass-like, vascular, flowering plants that are attached to the seafloor by extensive root systems. Seagrasses occur throughout the coastal areas of Florida, including protected bays and lagoons as well as deeper offshore waters on the continental shelf. Seagrasses have taken advantage of the broad, shallow shelf and clear water to produce two of the most extensive seagrass beds anywhere in continental North America.

Parameters

Percent Cover measures the fraction of an area of seafloor that is covered by SAV, usually estimated by evaluating multiple small areas of seafloor. Percent cover is often estimated for total SAV, individual types of vegetation (seagrass, attached algae, drift algae) and individual species.

Frequency of Occurrence was calculated as the number of times a taxon was observed in a year divided by the number of sampling events, multiplied by 100. Analysis is conducted at the quadrat level and is inclusive of all quadrats (i.e., quadrats evaluated using Braun-Blanquet, modified Braun-Blanquet, and percent cover.”

Species

Turtle grass (Thalassia testudinum) is the largest of the Florida seagrasses, with longer, thicker blades and deeper root structures than any of the other seagrasses. It is considered a climax seagrass species.

Shoal grass (Halodule wrightii) is an early colonizer of vegetated areas and usually grows in water too shallow for other species except widgeon grass. It can often tolerate larger salinity ranges than other seagrass species. Shoal grass is characterized by thin, flat blades, that are narrower than turtle grass blades.

Manatee grass (Syringodium filiforme) is easily recognizable because its leaves are thin and cylindrical instead of the flat, ribbon-like form shared by many other seagrass species. The leaves can grow up to half a meter in length. Manatee grass is usually found in mixed seagrass beds or small, dense monospecific patches.

Widgeon grass (Ruppia maritima) grows in both fresh and salt water and is widely distributed throughout Florida’s estuaries in less saline areas, particularly in inlets along the east coast. This species resembles shoal grass in certain environments but can be identified by the pointed tips of its leaves.

Three species of Halophila spp. are found in Florida - Star grass (Halophila engelmannii), Paddle grass (Halophila decipiens), and Johnson’s seagrass (Halophila johnsonii). These are smaller, more fragile seagrasses than other Florida species and are considered ephemeral. They grow along a single long rhizome, with short blades. These species are not well-studied, although surveys are underway to define their ecological roles.

Notes

Star grass, Paddle grass, and Johnson’s seagrass will be grouped together and listed as Halophila spp. in the following managed areas. This is because several surveys did not specify to the species level:

  • Banana River Aquatic Preserve

  • Indian River-Malabar to Vero Beach Aquatic Preserve

  • Indian River-Vero Beach to Ft. Pierce Aquatic Preserve

  • Jensen Beach to Jupiter Inlet Aquatic Preserve

  • Loxahatchee River-Lake Worth Creek Aquatic Preserve

  • Mosquito Lagoon Aquatic Preserve

  • Biscayne Bay Aquatic Preserve

  • Florida Keys National Marine Sanctuary

Maps showing the temporal scope of SAV sampling sites within the boundaries of Lemon Bay Aquatic Preserve by Program name.
Maps showing the temporal scope of SAV sampling sites within the boundaries of Lemon Bay Aquatic Preserve by Program name.

Click here to view spatio-temporal plots on GitHub.

Sampling locations by Program:

Map showing SAV sampling sites within the boundaries of Lemon Bay Aquatic Preserve. The point size reflects the number of samples at a given sampling site.
Map showing SAV sampling sites within the boundaries of Lemon Bay Aquatic Preserve. The point size reflects the number of samples at a given sampling site.
Program Information for Submerged Aquatic Vegetation
ProgramID N-Data YearMin YearMax method Sample Locations
570 2209 1998 2024 Braun Blanquet 6
568 1397 2007 2024 Percent Cover 10

Program names:

568 - Sarasota County Seagrass Monitoring9
570 - Charlotte Harbor Seagrass Monitoring10

Scatter plots of median percent cover of submerged aquatic vegetation over time by group. Plots for time series that included five or more years of observations show the estimated trend as a blue line.
Scatter plots of median percent cover of submerged aquatic vegetation over time by group. Plots for time series that included five or more years of observations show the estimated trend as a blue line.
Trends in median percent cover for various seagrass species in Lemon Bay Aquatic Preserve - simplified
Trends in median percent cover for various seagrass species in Lemon Bay Aquatic Preserve - simplified
Percent Cover Trend Analysis for Lemon Bay Aquatic Preserve
CommonName Trend Significance (0.05) Period of Record LME-Intercept LME-Slope p
Attached algae No significant trend 1999 - 2024 -1.172258 0.4710001 0.2600063
Drift algae Significantly decreasing trend 1999 - 2024 22.530993 -0.5442751 0.0227362
Shoal grass No significant trend 1998 - 2024 28.685694 0.1887747 0.5983172
No grass in quadrat Model did not fit the available data 1998 - 2024 - - -
Manatee grass No significant trend 1998 - 2024 6.783823 -0.0086613 0.9626967
Turtle grass No significant trend 1998 - 2024 4.315207 0.3038590 0.4537040
Total seagrass No significant trend 1998 - 2024 26.641958 0.5494435 0.2467879

An annual decrease in percent cover was observed for drift algae (-0.5%). Total seagrass, manatee grass, shoal grass, turtle grass, and attached algae showed no detectable change in percent cover.

Frequency of occurrence for various seagrass species in Lemon Bay Aquatic Preserve
Frequency of occurrence for various seagrass species in Lemon Bay Aquatic Preserve

SAV Water Column Analysis

The following parameters are available for Lemon Bay Aquatic Preserve within the SAV_WC_Report:

  • Colored Disolved Organic Matter

  • Chlorophyll a

  • Dissolved Oxygen

  • Dissolved Oxygen Saturation

  • pH

  • Salinity

  • Secchi Depth

  • Water Temperature

  • Total Nitrogen

  • Total Suspended Solids

  • Turbidity

Access the reports here: DRAFT_SAV_WC_Report_2024-11-20.pdf

Nekton

The data file used is: All_NEKTON_Parameters-2025-Sep-04.txt

Bar graph(s) of annual average nekton richness over time for species groups occurring in at least 1% of samples. The bar colors represent species groups including bony fishes, cartilaginous fishes, decapod crustaceans (e.g., shrimps, crabs, and lobsters), and cephalopods (e.g., squid). Gear types and sizes are indicated in the panel label.
Bar graph(s) of annual average nekton richness over time for species groups occurring in at least 1% of samples. The bar colors represent species groups including bony fishes, cartilaginous fishes, decapod crustaceans (e.g., shrimps, crabs, and lobsters), and cephalopods (e.g., squid). Gear types and sizes are indicated in the panel label.
Nekton Species Richness
Gear Type Sample Count Number of Years Period of Record Median N of Taxa Mean N of Taxa
Trawl (6.1) 6 1 2001 - 2001 0.74 0.93

The median annual number of taxa was 0.74 based on 6 observations collected by 6.1-meter trawl between 2001 and 2001.

Map showing location of nekton sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of nekton sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Oyster

The data file used is: All_OYSTER_Parameters-2025-Sep-04.txt

Density

Natural

Scatter plot of oyster density over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Scatter plot of oyster density over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Model results for Oyster Density - Natural
Shell Type Habitat Type Trend Status Estimate Standard Error Credible Interval
Live Oysters Natural Significantly decreasing trend -18.38 612.39 1.95 to 25.27

For natural reefs, density decreased by an average of 17.58 oysters per square meter per year.

Map showing location of oyster density sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of oyster density sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Percent Live

Natural

Scatter plot of percent live oysters over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Scatter plot of percent live oysters over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Model results for Oyster Percent Live - Natural
Shell Type Habitat Type Trend Status Estimate Standard Error Credible Interval
Live Oysters Natural Significantly decreasing trend 0 0.09 -0.01 to 0

For natural reefs, percent live cover decreased by an average of 0% per year.

Map showing location of oyster percent live sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of oyster percent live sampling locations within the boundaries of Lemon Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Species list

Acanthostracion quadricornis2 Eucinostomus gula2 Ocyurus chrysurus2
Achirus lineatus2 Eucinostomus harengulus2 Ogcocephalus cubifrons2
Albula spp.2 Eucinostomus spp.2 Ogcocephalus spp.2
Aluterus schoepfii2 Eugerres plumieri2 Oligoplites saurus2
Anarchopterus criniger2 Fistularia tabacaria2 Opisthonema oglinum2
Anchoa hepsetus2 Fundulus similis2 Opsanus beta2
Anchoa mitchilli2 Gobiesox strumosus2 Orthopristis chrysoptera2
Anchoa spp.2 Gobiosoma longipala2 Paralichthys albigutta2
Ancylopsetta quadrocellata2 Gobiosoma robustum2 Penaeus duorarum2
Archosargus probatocephalus2 Gobiosoma spp.2 Penicillus capitatus1
Ariopsis felis2 Haemulon plumierii2 Pogonias cromis2
Bagre marinus2 Halodule wrightii1 Prionotus rubio2
Bairdiella chrysoura2 Halophila engelmannii1 Prionotus scitulus2
Bathygobius soporator2 Harengula jaguana2 Prionotus tribulus2
Brevoortia spp.2 Hemiramphus brasiliensis2 Sciaenops ocellatus2
Calamus penna2 Hippocampus erectus2 Scomberomorus maculatus2
Callinectes sapidus2 Hippocampus zosterae2 Scorpaena brasiliensis2
Caranx hippos2 Hypleurochilus caudovittatus2 Selene vomer2
Caranx latus2 Hyporhamphus meeki2 Serraniculus pumilio2
Caulerpa mexicana1 Hyporhamphus unifasciatus2 Serranus subligarius2
Caulerpa prolifera1 Hypsoblennius hentz2 Sphoeroides nephelus2
Caulerpa sertularioides1 Lachnolaimus maximus2 Sphoeroides spengleri2
Caulerpa spp.1 Lagodon rhomboides2 Sphyraena barracuda2
Centropomus undecimalis2 Leiostomus xanthurus2 Strongylura marina2
Centropristis striata2 Limulus polyphemus Strongylura notata2
Chaetodipterus faber2 Lucania parva2 Symphurus plagiusa2
Chasmodes saburrae2 Lutjanus analis2 Syngnathus floridae2
Chilomycterus schoepfii2 Lutjanus griseus2 Syngnathus louisianae2
Chloroscombrus chrysurus2 Lutjanus synagris2 Syngnathus scovelli2
Citharichthys macrops2 Menippe spp.2 Syngnathus springeri2
Cynoscion arenarius2 Menticirrhus americanus2 Synodus foetens2
Cynoscion nebulosus2 Menticirrhus saxatilis2 Syringodium filiforme1
Diapterus auratus2 Microgobius gulosus2 Thalassia testudinum1
Diodon holocanthus2 Monacanthus ciliatus2 Total seagrass1
Diplectrum formosum2 Mugil cephalus2 Trachinotus carolinus2
Diplodus holbrookii2 Mugil curema2 Trachinotus falcatus2
Drift algae1 Mugil trichodon2 Trinectes maculatus2
Elops saurus2 Mycteroperca bonaci2 Tylosurus crocodilus2
Epinephelus itajara2 Mycteroperca microlepis2 Urophycis floridana2
Epinephelus morio2 Nicholsina usta2 Acanthostracion quadricornis2
Etropus crossotus2 No grass in quadrat1 Achirus lineatus2

1 - Submerged Aquatic Vegetation, 2 - Nekton

References

1.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Charlotte Harbor Aquatic Preserves. Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network. (2024).
2.
Florida Department of Environmental Protection (DEP). Florida STORET / WIN. (2024).
3.
Florida Fish and Wildlife Conservation Commission (FWC); Florida Fish and Wildlife Research Institute (FWRI). Harmful Algal Bloom Marine Observation Network. (2018).
4.
U.S. Environmental Protection Agency (EPA). EPA STOrage and RETrieval Data Warehouse (STORET)/WQX. (2023).
5.
U.S. Environmental Protection Agency (EPA); Office of Water; National Oceanic and Atmospheric Administration (NOAA); U.S. Geological Survey (USGS); U.S. Fish and Wildlife Service (USFWS); National Estuary Program (NEP); coastal states. National Aquatic Resource Surveys, National Coastal Condition Assessment. (2021).
6.
Florida Fish and Wildlife Conservation Commission (FWC). Fisheries-Independent Monitoring (FIM) Program. (2022).
7.
Southwest Florida Water Management District (SWFWMD). Southwest Florida Water Management District - Water Quality Monitoring. (2024).
8.
Charlotte Harbor National Estuary Program (CHNEP). Coastal Charlotte Harbor Monitoring Network. (2024).
9.
Sarasota County (Florida). Sarasota County Seagrass Monitoring. (2023).
10.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Charlotte Harbor Aquatic Preserves. Charlotte Harbor Seagrass Monitoring. (2023).