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 No significant trend 380 10 2012 - 2024 6 0.2398 2.5827 0.2345 0.0663

Chlorophyll a, corrected for pheophytin, showed no detectable trend between 2012 and 2024.

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor 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
514 321 2018 2024
5002 59 2012 2022

Program names:

514 - Florida LAKEWATCH Program1
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 Significantly increasing trend 1122 18 2001 - 2024 6.55 0.3032 3.2945 0.1684 0

Monthly average chlorophyll a, uncorrected for pheophytin, increased by 0.17 µg/L per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor 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
514 1103 2001 2024
5002 19 2019 2022

Program names:

514 - Florida LAKEWATCH Program1
5002 - Florida STORET / WIN2

Colored Dissolved Organic Matter - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average colored dissolved organic matter (CDOM) 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 CDOM (triangles) is included in the plot.
Scatter plot of monthly average colored dissolved organic matter (CDOM) 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 CDOM (triangles) is included in the plot.
Seasonal Kendall-Tau Trend Analysis for Colored Dissolved Organic Matter
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab Significantly increasing trend 423 18 2001 - 2024 8 0.232 6.6296 0.1922 0.0315

Monthly average colored dissolved organic matter increased by 0.19 PCU per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Colored Dissolved Organic Matter
ProgramID N_Data YearMin YearMax
514 423 2001 2024

Program names:

514 - Florida LAKEWATCH Program1

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 Significantly decreasing trend 8340 27 1998 - 2024 7.2 -0.1742 7.899 -0.033 0

Monthly average dissolved oxygen decreased by 0.03 mg/L per year.

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor 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 5829 1998 2022
69 1479 1998 2024
469 686 2016 2024
557 191 2005 2023
95 156 2004 2018

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program3
95 - Harmful Algal Bloom Marine Observation Network4
469 - Central Panhandle Aquatic Preserve WQ Monitoring5
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring6
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 5452 27 1998 - 2024 8.1 -0.1692 8.1428 -0.0067 0

Monthly average pH decreased by 0.01 pH units per year.

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor 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 2810 1998 2022
69 1455 1998 2024
469 686 2016 2024
558 180 2008 2014
557 170 2005 2023
95 152 2008 2018

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program3
95 - Harmful Algal Bloom Marine Observation Network4
469 - Central Panhandle Aquatic Preserve WQ Monitoring5
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring6
558 - Franklin County Coastal Waters Seagrass 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 9592 28 1996 - 2024 31.1 -0.1225 31.8061 -0.0494 0.0027

Monthly average salinity decreased by 0.05 ppt per year.

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor 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 6810 1998 2022
69 1477 1998 2024
469 686 2016 2024
558 258 2008 2014
557 191 2005 2023
95 171 1996 2018

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program3
95 - Harmful Algal Bloom Marine Observation Network4
469 - Central Panhandle Aquatic Preserve WQ Monitoring5
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring6
558 - Franklin County Coastal Waters Seagrass Monitoring7
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 No significant trend 3048 27 1998 - 2024 -1.2 0.0016 -1.2044 0 0.9487

Secchi depth showed no detectable trend between 1998 and 2024.

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor 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
69 1462 1998 2024
514 1126 2001 2024
558 331 2008 2017
557 105 2005 2023
5002 24 2019 2022

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program3
514 - Florida LAKEWATCH Program1
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring6
558 - Franklin County Coastal Waters Seagrass 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 Significantly increasing trend 1625 19 2001 - 2024 0.2 0.279 0.1205 0.0071 0

Monthly average total nitrogen increased by 0.01 mg/L per year.

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor 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
514 1175 2001 2024
5002 465 2001 2022

Program names:

514 - Florida LAKEWATCH Program1
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 increasing trend 1130 19 2001 - 2024 0 0.5583 -0.021 0.0012 0

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

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor 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
514 1149 2001 2024
5002 24 2012 2022

Program names:

514 - Florida LAKEWATCH Program1
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 Significantly decreasing trend 3543 18 1998 - 2022 5.3 -0.2432 6.5131 -0.1119 0.0012

Monthly average turbidity decreased by 0.11 NTU per year, indicating an increase in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor 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 3543 1998 2022
469 315 2021 2024
557 39 2022 2023

Program names:

469 - Central Panhandle Aquatic Preserve WQ Monitoring5
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring6
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 No significant trend 9833 28 1996 - 2024 25.9 -0.0219 23.0639 -0.0067 0.5819

Water temperature showed no detectable trend between 1996 and 2024.

Map showing location of discrete water quality sampling locations within the boundaries of Alligator Harbor 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 Alligator Harbor 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 7037 1998 2022
69 1483 1998 2024
469 686 2016 2024
558 271 2008 2017
557 191 2005 2023
95 166 1996 2018

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program3
95 - Harmful Algal Bloom Marine Observation Network4
469 - Central Panhandle Aquatic Preserve WQ Monitoring5
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring6
558 - Franklin County Coastal Waters Seagrass Monitoring7
5002 - Florida STORET / WIN2

Water Quality - Continuous

The following files were used in the continuous analysis:

  • Combined_WQ_WC_NUT_cont_Dissolved_Oxygen_NW-2025-Sep-19.txt

  • Combined_WQ_WC_NUT_cont_Dissolved_Oxygen_Saturation_NW-2025-Sep-19.txt

  • Combined_WQ_WC_NUT_cont_pH_NW-2025-Sep-19.txt

  • Combined_WQ_WC_NUT_cont_Salinity_NW-2025-Sep-19.txt

  • Combined_WQ_WC_NUT_cont_Turbidity_NW-2025-Sep-19.txt

  • Combined_WQ_WC_NUT_cont_Water_Temperature_NW-2025-Sep-19.txt

Continuous monitoring locations in Alligator Harbor Aquatic Preserve

Station overview for Continuous parameters by Program
ProgramID ProgramLocationID Years of Data Use in Analysis Parameters
468 CPAH 2 FALSE DO , DOS , pH , Sal , Turb , TempW
468 CPAH2 7 TRUE DO , DOS , pH , Sal , Turb , TempW
468 CPFS 5 TRUE DO , DOS , pH , Sal , Turb , TempW

Program names:

468 - Central Panhandle Aquatic Preserves Continuous Water Quality Monitoring8

Map showing continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. Sites marked as Use In Analysis (green) are featured in this report.
Map showing continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. Sites marked as Use In Analysis (green) are featured in this report.

Dissolved Oxygen - Continuous

Scatter plot of monthly average dissolved oxygen over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average dissolved oxygen over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Dissolved Oxygen - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
CPAH2 No significant trend 168824 7 2019 - 2025 6.8 -0.17 6.42 -0.05 0.1
CPAH Insufficient data to calculate trend 11557 2 2007 - 2008 8.0 - - - -
CPFS No significant trend 56853 5 2019 - 2023 6.4 0.12 6.36 0.06 0.74

No detectable change in monthly average dissolved oxygen was observed at two locations. There was insufficient data to fit a model for one location.

Map showing location of dissolved oxygen continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of dissolved oxygen continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Dissolved Oxygen Saturation - Continuous

Scatter plot of monthly average dissolved oxygen saturation over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average dissolved oxygen saturation over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Dissolved Oxygen Saturation - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
CPAH2 Significantly decreasing trend 168824 7 2019 - 2025 93.3 -0.2 93.99 -0.7 0.05
CPAH Insufficient data to calculate trend 11557 2 2007 - 2008 105.6 - - - -
CPFS No significant trend 56928 5 2019 - 2023 90.7 0.02 89.01 -0.24 1

At one program location, monthly average dissolved oxygen saturation decreased by 0.70% per year. No detectable change in monthly average dissolved oxygen saturation was observed at one location. There was insufficient data to fit a model for one location.

Map showing location of dissolved oxygen saturation continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of dissolved oxygen saturation continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

pH - Continuous

Scatter plot of monthly average pH over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average pH over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for pH - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
CPAH2 Significantly decreasing trend 166305 7 2019 - 2025 8.0 -0.25 8.01 -0.02 0.02
CPAH Insufficient data to calculate trend 13034 2 2007 - 2008 7.9 - - - -
CPFS No significant trend 61868 5 2019 - 2023 8.1 0.19 7.98 0.02 0.52

At one program location, monthly average pH decreased by 0.02 pH units per year. No detectable change in monthly average pH was observed at one location. There was insufficient data to fit a model for one location.

Map showing location of ph continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of ph continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Salinity - Continuous

Scatter plot of monthly average salinity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average salinity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Salinity - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
CPAH2 No significant trend 165044 7 2019 - 2025 31.0 0.14 30.87 0.18 0.25
CPAH Insufficient data to calculate trend 13034 2 2007 - 2008 34.0 - - - -
CPFS No significant trend 60346 5 2019 - 2023 30.5 0 29.87 0.13 1

No detectable change in monthly average salinity was observed at two locations. There was insufficient data to fit a model for one location.

Map showing location of salinity continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of salinity continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Turbidity - Continuous

Scatter plot of monthly average turbidity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average turbidity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Turbidity - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
CPAH2 No significant trend 169892 7 2019 - 2025 6 -0.08 10.61 -0.12 0.51
CPAH Insufficient data to calculate trend 12558 2 2007 - 2008 10 - - - -
CPFS No significant trend 55980 5 2019 - 2023 3 -0.16 11.21 -0.26 1

No detectable change in monthly average turbidity was observed at two locations. There was insufficient data to fit a model for one location.

Map showing location of turbidity continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of turbidity continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Water Temperature - Continuous

Scatter plot of monthly average water temperature over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average water temperature over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Water Temperature - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
CPAH2 No significant trend 182967 7 2019 - 2025 23.4 0.15 23.51 0.19 0.2
CPAH Insufficient data to calculate trend 13034 2 2007 - 2008 20.9 - - - -
CPFS Significantly increasing trend 80801 5 2019 - 2023 24.1 0.37 24.62 0.38 0.03

At one program location, monthly average water temperature increased by 0.38°C per year. No detectable change in monthly average water temperature was observed at one location. There was insufficient data to fit a model for one location.

Map showing location of water temperature continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of water temperature continuous water quality sampling locations within the boundaries of Alligator Harbor Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

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 Alligator Harbor Aquatic Preserve by Program name.
Maps showing the temporal scope of SAV sampling sites within the boundaries of Alligator Harbor 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 Alligator Harbor Aquatic Preserve. The point size reflects the number of samples at a given sampling site.
Map showing SAV sampling sites within the boundaries of Alligator Harbor 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
557 531 2008 2023 Braun Blanquet 16
558 2984 2009 2017 Percent Cover 38

Program names:

557 - Central Panhandle Aquatic Preserves Seagrass Monitoring6
558 - Franklin County Coastal Waters Seagrass Monitoring7

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 Alligator Harbor Aquatic Preserve - simplified
Trends in median percent cover for various seagrass species in Alligator Harbor Aquatic Preserve - simplified
Percent Cover Trend Analysis for Alligator Harbor Aquatic Preserve
CommonName Trend Significance (0.05) Period of Record LME-Intercept LME-Slope p
Drift algae Significantly decreasing trend 2009 - 2023 79.40292 -2.3562664 0.0273450
Shoal grass No significant trend 2008 - 2023 29.78764 -0.4993671 0.4716912
Star grass Insufficient data to calculate trend - - - -
No grass in quadrat Model did not fit the available data 2009 - 2023 - - -
Widgeon grass Insufficient data to calculate trend - - - -
Manatee grass Significantly decreasing trend 2008 - 2023 47.85836 -1.2281451 0.0253568
Turtle grass No significant trend 2008 - 2023 30.96903 -0.4530892 0.3778580

Annual decreases in percent cover were observed for manatee grass (-1.2%) and drift algae (-2.4%). No detectable change in percent cover was observed for shoal grass and turtle grass. Trends in percent cover could not be evaluated for star grass and widgeon grass due to insufficient data.

Frequency of occurrence for various seagrass species in Alligator Harbor Aquatic Preserve
Frequency of occurrence for various seagrass species in Alligator Harbor Aquatic Preserve

SAV Water Column Analysis

The following parameters are available for Alligator Harbor Aquatic Preserve within the SAV_WC_Report:

  • Colored Disolved Organic Matter

  • Chlorophyll a

  • Dissolved Oxygen

  • pH

  • Salinity

  • Secchi Depth

  • Water Temperature

  • Total Nitrogen

  • Turbidity

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

Species list

Acanthophora sp.1 Halodule wrightii1 Sargassum spp.1
Caulerpa prolifera1 Halophila engelmannii1 Syringodium filiforme1
Drift algae1 Hypnea1 Thalassia testudinum1
Drift red algae1 No grass in quadrat1 Yuzurua poiteaui1
Gracilaria sp.1 Ruppia maritima1 Acanthophora sp.1

1 - Submerged Aquatic Vegetation

References

1.
University of Florida (UF); Institute of Food and Agricultural Sciences. Florida LAKEWATCH Program. (2024).
2.
Florida Department of Environmental Protection (DEP). Florida STORET / WIN. (2024).
3.
Florida Fish and Wildlife Conservation Commission (FWC). Fisheries-Independent Monitoring (FIM) Program. (2022).
4.
Florida Fish and Wildlife Conservation Commission (FWC); Florida Fish and Wildlife Research Institute (FWRI). Harmful Algal Bloom Marine Observation Network. (2018).
5.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Central Panhandle Aquatic Preserves. Central Panhandle Aquatic Preserve WQ Monitoring . (2024).
6.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Central Panhandle Aquatic Preserves. Central Panhandle Aquatic Preserves Seagrass Monitoring. (2023).
7.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Central Panhandle Aquatic Preserves; Florida Fish and Wildlife Conservation Commission (FWC). Franklin County Coastal Waters Seagrass Monitoring. (2017).
8.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Central Panhandle Aquatic Preserves. Central Panhandle Aquatic Preserves Continuous Water Quality Monitoring. (2024).