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: 2026-06-10

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
Chlorophyll a, Uncorrected for Pheophytin ug/L - -
Dissolved Oxygen mg/L -0.000001 50
Dissolved Oxygen Saturation % -0.000001 500
Fluorescent Dissolved Organic Matter QSE - -
Salinity ppt -0.000001 70
Specific Conductivity mS/cm -0.000001 200
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 (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, inorganic 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 Ammonia (N) mg/L - -
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-2026-May-18.txt

  • Combined_WQ_WC_NUT_Chlorophyll_a_uncorrected_for_pheophytin-2026-May-18.txt

  • Combined_WQ_WC_NUT_Colored_dissolved_organic_matter_CDOM-2026-May-18.txt

  • Combined_WQ_WC_NUT_Dissolved_Oxygen-2026-May-18.txt

  • Combined_WQ_WC_NUT_Dissolved_Oxygen_Saturation-2026-May-18.txt

  • Combined_WQ_WC_NUT_pH-2026-May-18.txt

  • Combined_WQ_WC_NUT_Salinity-2026-May-18.txt

  • Combined_WQ_WC_NUT_Secchi_Depth-2026-May-18.txt

  • Combined_WQ_WC_NUT_Total_Nitrogen-2026-May-18.txt

  • Combined_WQ_WC_NUT_Total_Phosphorus-2026-May-18.txt

  • Combined_WQ_WC_NUT_Total_Suspended_Solids_TSS-2026-May-18.txt

  • Combined_WQ_WC_NUT_Turbidity-2026-May-18.txt

  • Combined_WQ_WC_NUT_Water_Temperature-2026-May-18.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 No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
Lab Increasing trend 2942 19 2000 - 2025 9.3 0.4012 3.1155 0.401 0

Monthly average chlorophyll a, corrected for pheophytin, increased by 0.4 µg/L per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola 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 Apalachicola 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
355 2462 2013 2025
5002 500 2000 2025

Program names:

355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring 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 No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
Lab Increasing trend 2571 21 2002 - 2025 12 0.3612 3.5002 0.4944 0

Monthly average chlorophyll a, uncorrected for pheophytin, increased by 0.49 µg/L per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola 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 Apalachicola 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
355 2463 2013 2025
5002 62 2012 2025
514 51 2007 2008
103 9 2002 2015
118 5 2005 2010
115 2 2002 2004

Program names:

355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
5002 - Florida STORET / WIN2
514 - Florida LAKEWATCH Program3
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
115 - Environmental Monitoring Assessment Program6

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 No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
Field Decreasing trend 53650 34 1992 - 2025 7.5 -0.0831 7.535 -0.0097 0.0238

Monthly average dissolved oxygen decreased by 0.01 mg/L per year.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola 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 Apalachicola 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
69 26205 1998 2024
5002 22424 1995 2025
129 3559 2000 2025
355 2012 2011 2025
95 256 1995 2018
557 121 2006 2023
118 52 2005 2020
115 16 1992 2004
103 15 2015 2015
119 14 1994 1994
5071 3 2017 2017

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program7
5002 - Florida STORET / WIN2
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring8
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
95 - Harmful Algal Bloom Marine Observation Network9
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring10
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
115 - Environmental Monitoring Assessment Program6
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
119 - National Status and Trends Bioeffects program11
5071 - Oyster shell heights and taxonomic diversity in 2015-2017 among previously documented oiled and non-oiled reefs in Louisiana, Alabama, and the Florida panhandle12

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 No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
Field Increasing trend 4593 26 2000 - 2025 92.7 0.19 87.1556 0.3435 0

Monthly average dissolved oxygen saturation increased by 0.34% per year.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola 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 Apalachicola 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
129 3545 2000 2025
355 910 2011 2023
5002 148 2003 2025

Program names:

129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring8
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
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 No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
Field Decreasing trend 42704 35 1964 - 2025 8 -0.2972 8.2848 -0.009 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 Apalachicola 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 Apalachicola 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
69 26253 1998 2024
5002 13201 1995 2025
129 2117 2000 2025
355 1805 2011 2025
95 184 1964 2018
557 110 2006 2023
115 16 1992 2004
103 16 2015 2015

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program7
5002 - Florida STORET / WIN2
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring8
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
95 - Harmful Algal Bloom Marine Observation Network9
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring10
115 - Environmental Monitoring Assessment Program6
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4

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 No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
All Decreasing trend 62489 37 1964 - 2025 15.8 -0.1561 21.6193 -0.1129 0

Monthly average salinity decreased by 0.11 ppt per year.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola 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 Apalachicola 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 31052 1995 2024
69 26393 1998 2024
129 3564 2000 2025
355 1894 2011 2024
95 373 1964 2018
557 121 2006 2023
456 33 2005 2013
115 16 1992 2004
119 14 1994 1994
5071 3 2017 2017

Program names:

5002 - Florida STORET / WIN2
69 - Fisheries-Independent Monitoring (FIM) Program7
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring8
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
95 - Harmful Algal Bloom Marine Observation Network9
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring10
456 - Oyster Sentinel13
115 - Environmental Monitoring Assessment Program6
119 - National Status and Trends Bioeffects program11
5071 - Oyster shell heights and taxonomic diversity in 2015-2017 among previously documented oiled and non-oiled reefs in Louisiana, Alabama, and the Florida panhandle12

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 No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
Lab Increasing trend 2874 25 1992 - 2025 0.611 0.1175 0.5487 0.0034 0.0286

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

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola 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 Apalachicola 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
355 2382 2013 2025
5002 421 1992 2025
514 50 2007 2008
103 19 2002 2015
115 2 2002 2004

Program names:

355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
5002 - Florida STORET / WIN2
514 - Florida LAKEWATCH Program3
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
115 - Environmental Monitoring Assessment Program6

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 No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
Lab No detectable trend 2977 24 1992 - 2025 0.031 0.0669 0.0255 0.0001 0.2553

Total phosphorus showed no detectable trend between 1992 and 2025.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola 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 Apalachicola 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
355 2492 2013 2025
5002 497 1992 2025
514 50 2007 2008
103 14 2002 2015
115 2 2002 2004

Program names:

355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
5002 - Florida STORET / WIN2
514 - Florida LAKEWATCH Program3
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
115 - Environmental Monitoring Assessment Program6

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 No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
Lab No detectable trend 15924 28 1992 - 2025 5.6 -0.0189 6.516 -0.0068 0.7401

Turbidity showed no detectable trend between 1992 and 2025.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola 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 Apalachicola 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 15923 1992 2025
129 2096 2000 2025
355 520 2011 2019
103 3 2005 2006

Program names:

5002 - Florida STORET / WIN2
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring8
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4

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 No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
Field Increasing trend 62742 37 1964 - 2025 24 0.1088 21.0423 0.0216 0.0033

Monthly average water temperature increased by 0.02°C per year.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola 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 Apalachicola 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 31197 1995 2025
69 26484 1998 2024
129 3558 2000 2025
355 2014 2011 2025
95 332 1964 2018
557 121 2006 2023
456 33 2005 2013
115 16 1992 2004
119 14 1994 1994
5071 3 2017 2017

Program names:

5002 - Florida STORET / WIN2
69 - Fisheries-Independent Monitoring (FIM) Program7
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring8
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
95 - Harmful Algal Bloom Marine Observation Network9
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring10
456 - Oyster Sentinel13
115 - Environmental Monitoring Assessment Program6
119 - National Status and Trends Bioeffects program11
5071 - Oyster shell heights and taxonomic diversity in 2015-2017 among previously documented oiled and non-oiled reefs in Louisiana, Alabama, and the Florida panhandle12

Water Quality - Continuous

The following files were used in the continuous analysis:

  • Combined_WQ_WC_NUT_cont_Chlorophyll_a_Uncorrected_for_Pheophytin-2026-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Dissolved_Oxygen-2026-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Dissolved_Oxygen_Saturation-2026-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Fluorescent_Dissolved_Organic_Matter-2026-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_pH-2026-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Salinity-2026-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Specific_Conductivity-2026-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Turbidity-2026-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Water_Temperature-2026-Mar-06.txt

Continuous monitoring locations in Apalachicola Bay Aquatic Preserve

Station overview for Continuous parameters by Program
ProgramID ProgramLocationID Years of Data Use in Analysis Parameters
355 apadbwq 25 TRUE pH , Dissolved Oxygen Saturation, Dissolved Oxygen , Turbidity , Water Temperature , Salinity , Specific Conductivity
355 apaebwq 30 TRUE Turbidity
355 apaebwq 32 TRUE pH , Dissolved Oxygen Saturation, Dissolved Oxygen , Water Temperature , Salinity , Specific Conductivity
355 apaeswq 31 TRUE Turbidity
355 apaeswq 32 TRUE pH , Dissolved Oxygen Saturation, Dissolved Oxygen , Water Temperature , Salinity , Specific Conductivity
355 apalmwq 11 TRUE pH , Dissolved Oxygen Saturation, Dissolved Oxygen , Turbidity , Water Temperature , Salinity , Specific Conductivity
355 apapcwq 11 TRUE pH , Dissolved Oxygen Saturation, Dissolved Oxygen , Turbidity , Water Temperature , Salinity , Specific Conductivity

Program names:

355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1

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

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
Program Location Statistical Trend No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
apadbwq Significantly decreasing trend 636788 25 2002 - 2026 8.0 -0.11 8.06 0.00 0.01
apaebwq Significantly decreasing trend 754923 32 1995 - 2026 7.6 -0.11 7.63 -0.01 0.00
apaeswq Significantly decreasing trend 745836 32 1995 - 2026 7.5 -0.10 7.58 -0.01 0.01
apalmwq No significant trend 297196 11 2016 - 2026 7.1 -0.06 7.13 0.00 0.50
apapcwq Significantly decreasing trend 302765 11 2016 - 2026 8.1 -0.35 8.16 -0.02 0.00

At four program locations, monthly average pH decreased between less than 0.01 and 0.02 pH units per year. No detectable change in monthly average pH was observed at one location.

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
Program Location Statistical Trend No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
apadbwq No significant trend 658527 25 2002 - 2026 94.9 -0.05 97.62 -0.08 0.27
apaebwq Significantly decreasing trend 694367 32 1995 - 2026 84.9 -0.23 91.03 -0.60 0.00
apaeswq No significant trend 746726 32 1995 - 2026 84.5 -0.06 85.63 -0.15 0.10
apalmwq Significantly decreasing trend 289599 11 2016 - 2026 74.9 -0.16 76.47 -0.51 0.04
apapcwq No significant trend 305661 11 2016 - 2026 94.0 0.04 92.74 0.11 0.54

At two program locations, monthly average dissolved oxygen saturation decreased by 0.51% per year at one site and by 0.6% per year at the other. No detectable change in monthly average dissolved oxygen saturation was observed at three locations.

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
Program Location Statistical Trend No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
apadbwq Significantly decreasing trend 654044 25 2002 - 2026 7.3 -0.11 7.57 -0.01 0.01
apaebwq Significantly decreasing trend 698115 32 1995 - 2026 6.8 -0.27 7.55 -0.06 0.00
apaeswq Significantly decreasing trend 745989 32 1995 - 2026 6.8 -0.10 7.04 -0.02 0.01
apalmwq Significantly decreasing trend 289063 11 2016 - 2026 6.3 -0.16 6.74 -0.05 0.04
apapcwq No significant trend 302205 11 2016 - 2026 6.9 -0.03 6.98 -0.01 0.79

At four program locations, monthly average dissolved oxygen decreased between 0.01 and 0.06 mg/L per year. No detectable change in monthly average dissolved oxygen was observed at one location.

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
Program Location Statistical Trend No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
apadbwq No significant trend 638719 25 2002 - 2026 10 0.05 16.21 0.06 0.23
apaebwq Significantly decreasing trend 672490 28 1997 - 2026 13 -0.18 19.33 -0.18 0.00
apaeswq Significantly decreasing trend 735494 31 1996 - 2026 9 -0.13 11.31 -0.09 0.00
apalmwq No significant trend 275282 11 2016 - 2026 11 0.08 11.53 0.23 0.36
apapcwq No significant trend 292616 11 2016 - 2026 7 -0.11 10.95 -0.15 0.15

At two program locations, monthly average turbidity decreased by 0.09 NTU per year at one site and by 0.18 NTU per year at the other. No detectable change in monthly average turbidity was observed at three locations.

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
Program Location Statistical Trend No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
apadbwq Significantly increasing trend 679646 25 2002 - 2026 23.3 0.16 22.86 0.03 0.00
apaebwq Significantly increasing trend 799283 32 1995 - 2026 24.1 0.16 23.05 0.02 0.00
apaeswq Significantly increasing trend 800593 32 1995 - 2026 24.1 0.20 22.88 0.04 0.00
apalmwq No significant trend 307034 11 2016 - 2026 22.7 0.01 23.35 0.00 0.93
apapcwq No significant trend 308627 11 2016 - 2026 23.2 0.00 23.62 -0.01 0.98

At three program locations, monthly average water temperature increased between 0.02 and 0.04°C per year. No detectable change in monthly average water temperature was observed at two locations.

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
Program Location Statistical Trend No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
apadbwq No significant trend 651798 25 2002 - 2026 22.3 0.00 21.84 -0.01 0.93
apaebwq No significant trend 782974 32 1995 - 2026 10.0 0.04 9.24 0.02 0.32
apaeswq No significant trend 792598 32 1995 - 2026 7.6 0.05 6.97 0.03 0.18
apalmwq Significantly increasing trend 304777 11 2016 - 2026 0.1 0.24 0.08 0.01 0.00
apapcwq No significant trend 303665 11 2016 - 2026 27.1 0.14 25.99 0.25 0.07

At one program location, monthly average salinity increased by 0.01 ppt per year. No detectable change in monthly average salinity was observed at four locations.

Specific Conductivity - Continuous

Scatter plot of monthly average specific conductivity 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 specific conductivity 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 Specific Conductivity - All Stations
Program Location Statistical Trend No. of Samples No. Years with Data Period of Record Median Result Value Tau Sen Intercept Sen Slope P
apadbwq No significant trend 651297 25 2002 - 2026 35.35 -0.01 34.64 -0.01 0.86
apaebwq No significant trend 783182 32 1995 - 2026 16.97 0.04 15.57 0.03 0.32
apaeswq No significant trend 792928 32 1995 - 2026 13.14 0.05 12.34 0.04 0.20
apalmwq Significantly increasing trend 304777 11 2016 - 2026 0.15 0.24 0.12 0.02 0.00
apapcwq No significant trend 303667 11 2016 - 2026 42.28 0.15 40.60 0.35 0.06

At one program location, monthly average specific conductivity increased by 0.02 mS/cm per year. No detectable change in monthly average specific conductivity was observed at four locations.

Submerged Aquatic Vegetation

The data file used is: All_SAV_Parameters-2026-Jun-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 Apalachicola Bay Aquatic Preserve by program name.
Maps showing the temporal scope of SAV sampling sites within the boundaries of Apalachicola 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 Apalachicola 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 Apalachicola 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
557 308 2008 2023 Braun Blanquet 21
997 79 2003 2003 Braun Blanquet 4
997 81 2003 2003 Percent Cover 4

Program names:

557 - Central Panhandle Aquatic Preserves Seagrass Monitoring10
997 - Apalachicola Bay Ephemeral SAV Monitoring14

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.
Trend lines of median percent cover of submerged aquatic vegetation over time for species that had five or more years of observations. Line type represents significance (solid) or non-significance (dashed) of the trends.
Trend lines of median percent cover of submerged aquatic vegetation over time for species that had five or more years of observations. Line type represents significance (solid) or non-significance (dashed) of the trends.
Percent Cover Trend Analysis for Apalachicola Bay Aquatic Preserve
Species Statistical Trend Period of Record LME Intercept LME Slope P
Drift algae Decreasing trend 2003 - 2023 84.82195 -2.630957 0.0014344
Shoal grass No detectable trend 2008 - 2023 31.68994 0.916393 0.4876112
Widgeon grass Insufficient data - - - -

An annual decrease in percent cover was observed for drift algae (-2.63%). No detectable change in percent cover was observed for shoal grass. Trends in percent cover could not be evaluated for widgeon grass due to insufficient data.

Bar plot of submerged aquatic vegetation species occurrence frequency over time by group.
Bar plot of submerged aquatic vegetation species occurrence frequency over time by group.

SAV Water Column Analysis

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

  • 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.pdf

Nekton

The data file used is: All_NEKTON_Parameters-2026-Jun-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 No. of Samples No. of Years with Data Period of Record Median No. of Taxa Mean No. of Taxa
Trawl (4.8 m) 5054 25 2000 - 2025 0.74 1.13

The median annual number of taxa was 0.74 based on 5,054 observations collected by 4.8-meter trawl between 2000 and 2025.

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

Coastal Wetlands

The data file used is: All_CW_Parameters-2026-Jun-04.txt

Line graph of annual average coastal wetlands species richness over time for mangroves and associates (triangles), marsh (squares), and marsh succulents (circles). If the time series by species group included more than one year of observations, a line connects data points for visualization.
Line graph of annual average coastal wetlands species richness over time for mangroves and associates (triangles), marsh (squares), and marsh succulents (circles). If the time series by species group included more than one year of observations, a line connects data points for visualization.
Coastal Wetlands Species Richness
Species Group No. of Samples No. Years with Data Period of Record Median No. of Taxa Mean No. of Taxa
Mangroves and associates 4 2 2022 - 2023 1.0 1.00
Marsh 144 10 2014 - 2023 1.5 2.08
Marsh succulents 56 10 2014 - 2023 3.0 2.20

Between 2022 and 2023, the median annual number of species for mangroves and associates was 1 based on 4 observations. Between 2014 and 2023, the median annual number of species for marsh was 1.5 based on 144 observations. Between 2014 and 2023, the median annual number of species for marsh succulents was 3 based on 56 observations.

Map showing location of coastal wetlands sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of coastal wetlands sampling locations within the boundaries of Apalachicola 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-2026-Jun-04.txt

Maps showing the temporal scope of oyster sampling sites within the boundaries of Apalachicola Bay Aquatic Preserve by program name.
Maps showing the temporal scope of oyster sampling sites within the boundaries of Apalachicola Bay Aquatic Preserve by program name.

Click here to view spatio-temporal plots on GitHub.

Density

For natural reefs, density showed no detectable trend between 2010 and 2016. For restored reefs, density showed no detectable trend between 2016 and 2023.

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
Habitat Type Shell Type Statistical Trend Period of Record Estimate Standard Error Credible Interval
Natural Live Oysters No detectable trend 2010 - 2016 -20.88 42.92 -114.54 to 7.94

Restored

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 - Restored
Habitat Type Shell Type Statistical Trend Period of Record Estimate Standard Error Credible Interval
Restored Live Oysters No detectable trend 2016 - 2023 -3 2.77 -7.47 to 3
Map showing location of oyster density sampling locations within the boundaries of Apalachicola 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 Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Percent Live

For natural reefs, percent live cover increased by an average of 2.37% per year. For restored reefs, percent live cover decreased by an average of 1.77% per year.

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. Estimation method is represented as percent (circles), point-intercept (triangle), or estimated percent (square), with data points 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. Estimation method is represented as percent (circles), point-intercept (triangle), or estimated percent (square), with data points jittered horizontally to reduce overlap.
Model results for Oyster Percent Live - Natural
Habitat Type Shell Type Statistical Trend Period of Record Estimate Standard Error Credible Interval
Natural Live Oysters Increasing trend 2018 - 2024 2.37 0.33 1.72 to 3.02

Restored

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. Estimation method is represented as percent (circles), point-intercept (triangle), or estimated percent (square), with data points 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. Estimation method is represented as percent (circles), point-intercept (triangle), or estimated percent (square), with data points jittered horizontally to reduce overlap.
Model results for Oyster Percent Live - Restored
Habitat Type Shell Type Statistical Trend Period of Record Estimate Standard Error Credible Interval
Restored Live Oysters Decreasing trend 2016 - 2023 -1.77 0.35 -2.47 to -1.09
Map showing location of oyster percent live sampling locations within the boundaries of Apalachicola 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 Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Shell Height

For natural reefs, there was insufficient data to calculate a trend for live oysters in either the 25-75mm or the ≥75mm size class. For restored reefs, there was no detectable trend for live oysters in either the 25-75mm or the ≥75mm size class. Models are not run on dead oyster shell measurements.

Natural

Model results for Oyster Shell Height - Natural
Habitat Type Shell Type SizeClass Statistical Trend Period of Record No. of Samples Estimate Standard Error Credible Interval
Natural Dead Oyster Shells >75mm Model not run on dead oyster shell 1621 - 1993 16 - - -
Natural Dead Oyster Shells 25-75mm Model not run on dead oyster shell 1621 - 2002 1460 - - -
Natural Live Oysters >75mm Insufficient data 2013 - 2016 21 - - -
Natural Live Oysters 25-75mm Insufficient data 2013 - 2017 256 - - -

Restored

Model results for Oyster Shell Height - Restored
Habitat Type Shell Type SizeClass Statistical Trend Period of Record No. of Samples Estimate Standard Error Credible Interval
Restored Live Oysters >75mm Model did not fit the available data 1982 - 2023 19751 - - -
Restored Live Oysters 25-75mm Model did not fit the available data 1982 - 2023 121890 - - -
Map showing location of oyster shell height sampling locations within the boundaries of Apalachicola 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 shell height sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Species list

Acanthostracion lactrophyrs3 Galium tinctorium Pagurus pollicaris3
Acanthostracion quadricornis3 Gambusia holbrooki3 Pagurus spp.3
Acer rubrum Gerres cinereus3 Palaemon floridanus3
Acetabularia crenulata1 Gobiesox strumosus3 Palaemon mundusnovus3
Acetes americanus3 Gobiidae spp.3 Palaemon pugio3
Achelous gibbesii3 Gobioides broussonnetii3 Palaemon spp.3
Achelous spinimanus3 Gobionellus oceanicus3 Palaemon vulgaris3
Achirus lineatus3 Gobionellus spp.3 Panicum repens
Acipenser oxyrinchus3 Gobiosoma bosc3 Panicum virgatum
Agalinis maritima Gobiosoma longipala3 Panopeus herbstii3
Albula vulpes3 Gobiosoma robustum3 Parablennius marmoreus3
Alosa alabamae3 Gobiosoma spp.3 Paralichthyidae spp.3
Alosa chrysochloris3 Gracilaria sp.1 Paralichthys albigutta3
Alosa spp.3 Gymnura micrura3 Paralichthys lethostigma3
Alpheus armillatus3 Haemulon aurolineatum3 Paralichthys spp.3
Alpheus estuariensis3 Haemulon plumierii3 Paralichthys squamilentus3
Alpheus heterochaelis3 Halichoeres bivittatus3 Parapenaeus politus3
Alpheus normanni3 Halodule wrightii1 Paspalum vaginatum2
Alternanthera philoxeroides Harengula jaguana3 Pattalias palustre
Aluterus schoepfii3 Hemicaranx amblyrhynchus3 Penaeidae3
Aluterus scriptus3 Hemipholis elongata Penaeus aztecus3
Aluterus spp.3 Hepatus epheliticus3 Penaeus duorarum3
Amaranthus cannabinus Heterandria formosa3 Penaeus setiferus3
Ambidexter symmetricus3 Hexapanopeus angustifrons3 Penaeus sp.3
Ameiurus catus3 Hippocampus erectus3 Penaeus spp.3
Ameiurus natalis3 Hippocampus zosterae3 Peprilus burti3
Ameiurus nebulosus3 Hippolyte zostericola3 Peprilus paru3
Ameiurus spp.3 Hydrilla verticillata Peprilus spp.3
Amia calva3 Hydrocotyle umbellata Percidae spp.3
Ampelaster carolinianus Hypanus americanus3 Persea palustris
Anarchopterus criniger3 Hypanus sabinus3 Persephona mediterranea3
Anchoa cubana3 Hypanus say3 Persicaria hydropiperoides
Anchoa hepsetus3 Hypleurochilus geminatus3 Petrolisthes armatus3
Anchoa lyolepis3 Hypleurochilus spp.3 Phragmites berlandieri
Anchoa mitchilli3 Hyporhamphus meeki3 Physalis angustifolia
Anchoa sp.3 Hyporhamphus spp.3 Physostegia leptophylla
Anchoa spp.3 Hypsoblennius hentz3 Pilumnus sayi3
Ancylopsetta quadrocellata3 Hypsoblennius ionthas3 Pinnixa spp.3
Anguilla rostrata3 Ictaluridae spp.3 Poaceae sp.
Aphredoderus sayanus3 Ictalurus furcatus3 Pogonias cromis3
Archosargus probatocephalus3 Ictalurus punctatus3 Polygonum hydropiperoides
Ariopsis felis3 Ictalurus spp.3 Polypremum procumbens
Aristida sp. Ilex vomitoria Pomatomus saltatrix3
Astroscopus ygraecum3 Ipomoea sagittata Pomoxis nigromaculatus3
Baccharis halimifolia Iris virginica Pontederia cordata
Bagre marinus3 Iva frutescens Porichthys plectrodon3
Bairdiella chrysoura3 Juncus acuminatus2 Portunidae spp.3
Bare substrate Juncus roemerianus2 Portunus sayi3
Bathygobius soporator3 Juncus scirpoides2 Potamogeton pusillus
Batis maritima2 Juncus spp.2 Prionotus alatus3
Belzebub faxoni3 Juncus validus2 Prionotus longispinosus3
Bidens mitis Kosteletzkya pentacarpos Prionotus rubio3
Blutaparon vermiculare2 Kyphosus sectatrix3 Prionotus scitulus3
Bolboschoenus robustus Lactophrys trigonus3 Prionotus spp.3
Borrichia frutescens Lactophrys triqueter3 Prionotus tribulus3
Bothidae spp.3 Lagocephalus laevigatus3 Processa hemphilli3
Brachyura3 Lagodon rhomboides3 Ptilimnium capillaceum
Brevoortia spp.3 Larimus fasciatus3 Quercus marilandica
Brotula barbata3 Latreutes parvulus3 Quercus minima
Brown algae1 Leander tenuicornis3 Quercus muehlenbergii
Calamus arctifrons3 Legume sp. Rachycentron canadum3
Calappa ocellata3 Leiostomus xanthurus3 Raja eglanteria3
Callinectes sapidus3 Lepisosteus oculatus3 Remora remora3
Callinectes similis3 Lepisosteus osseus3 Rhinoptera bonasus3
Callinectes spp.3 Lepomis auritus3 Rhithropanopeus harrisii3
Campsis radicans Lepomis gulosus3 Rhizophora mangle2
Carangidae spp.3 Lepomis macrochirus3 Rhizoprionodon terraenovae3
Caranx crysos3 Lepomis microlophus3 Rimapenaeus constrictus3
Caranx hippos3 Lepomis punctatus3 Rimapenaeus similis3
Caranx latus3 Lepomis spp.3 Rimapenaeus spp.3
Caranx ruber3 Leptochela serratorbita3 Rumex verticillatus
Caranx spp.3 Libinia dubia3 Ruppia maritima1
Carcharhinus limbatus3 Limonium carolinianum2 Sabal palmetto
Carex hyalinolepis Limulus polyphemus Sagittaria graminea
Carex joorii Lithadia granulosa3 Salicornia ambigua2
Carex sp. Lobotes surinamensis3 Salvinia spp.
Carpiodes carpio3 Lolliguncula brevis3 Sardinella aurita3
Centella asiatica Lucania parva3 Saururus cernuus
Centrarchidae spp.3 Ludwigia repens Schoenoplectus americanus
Centrarchus macropterus3 Luidia clathrata Schoenoplectus californicus
Centropristis ocyurus3 Lutjanus campechanus3 Sciaenidae spp.3
Centropristis philadelphica3 Lutjanus griseus3 Sciaenops ocellatus3
Centropristis striata3 Lutjanus sp.3 Scomberomorus maculatus3
Cephalanthus occidentalis Lutjanus spp.3 Scorpaena brasiliensis3
Ceratophyllum demersum Lutjanus synagris3 Selene setapinnis3
Chaetodipterus faber3 Lycopus virginicus Selene vomer3
Chara spp.1 Lysmata wurdemanni3 Serraniculus pumilio3
Chasmodes saburrae3 Lythrum lineare Serranus subligarius3
Chilomycterus schoepfii3 Macrobrachium ohione3 Sesbania punicea
Chloroscombrus chrysurus3 Megalops atlanticus3 Sesbania vesicaria
Cicuta maculata Melongena corona Sesuvium portulacastrum2
Citharichthys macrops3 Membras martinica3 Setaria parviflora
Citharichthys sp.3 Menidia beryllina3 Sicyonia brevirostris3
Citharichthys spilopterus3 Menidia sp.3 Sicyonia dorsalis3
Citharichthys spp.3 Menidia spp.3 Sicyonia laevigata3
Cladium mariscus Menippe mercenaria3 Smilax auriculata
Clibanarius vittatus3 Menticirrhus americanus3 Smilax bona-nox
Crinum americanum Menticirrhus littoralis3 Smilax walteri
Ctenogobius boleosoma3 Menticirrhus saxatilis3 Solidago sempervirens
Ctenogobius shufeldti3 Menticirrhus spp.3 Sparidae spp.3
Ctenogobius spp.3 Metoporhaphis calcarata3 Spartina alterniflora2
Ctenogobius stigmaticus3 Microgobius gulosus3 Spartina cynosuroides2
Ctenopharyngodon idella3 Microgobius microlepis3 Spartina patens2
Cuapetes americanus3 Microgobius sp.3 Sphoeroides nephelus3
Cynoscion arenarius3 Microgobius spp.3 Sphoeroides parvus3
Cynoscion nebulosus3 Microgobius thalassinus3 Sphoeroides spengleri3
Cynoscion nothus3 Microphis brachyurus3 Sphoeroides spp.3
Cynoscion spp.3 Micropogonias undulatus3 Sphyraena barracuda3
Cyperaceae sp. Micropterus salmoides3 Sphyraena borealis3
Cyperus haspan Mikania scandens Sphyraena guachancho3
Cyperus sp. Minytrema melanops3 Sphyraena spp.3
Cyprinidae spp.3 Monacanthus ciliatus3 Sphyrna tiburo3
Cyprinodon variegatus3 Morone chrysops x saxatilis3 Sporobolus virginicus2
Cyprinus carpio3 Morone hybrid3 Squilla empusa
Dasyatis sp.3 Morone saxatilis3 Stellifer lanceolatus3
Diapterus auratus3 Morone spp.3 Stenotomus caprinus3
Dichanthelium sp. Moxostoma spp.3 Stephanolepis hispida3
Diplectrum bivittatum3 Mugil cephalus3 Strongylura marina3
Diplectrum formosum3 Mugil curema3 Strongylura notata3
Diplectrum spp.3 Mugil spp.3 Strongylura spp.3
Diplodus holbrookii3 Muhlenbergia capillaris Strongylura timucu3
Distichlis spicata2 Mycteroperca microlepis3 Suaeda linearis2
Dormitator maculatus3 Mycteroperca phenax3 Syacium papillosum3
Dorosoma cepedianum3 Mycteroperca spp.3 Symphurus parvus3
Dorosoma petenense3 Myrica cerifera Symphurus plagiusa3
Dorosoma spp.3 Myrophis punctatus3 Symphyotrichum tenuifolium
Drift algae1 Najas guadalupensis Syngnathus floridae3
Dyspanopeus texanus3 Neopanope packardii3 Syngnathus louisianae3
Echeneis naucrates3 Neverita duplicata Syngnathus scovelli3
Echeneis neucratoides3 Nicholsina usta3 Syngnathus spp.3
Echeneis spp.3 No fish Synodus foetens3
Echiophis punctifer3 No grass in quadrat1 Synodus spp.3
Edrastima uniflora Notemigonus crysoleucas3 Taxodium distichum
Eleocharis fallax Notropis maculatus3 Toxicodendron radicans
Eleotris amblyopsis3 Notropis spp.3 Tozeuma carolinense3
Elopidae3 Oenothera simulans Trachinotus carolinus3
Elops saurus3 Ogcocephalus corniger3 Trachinotus falcatus3
Elops smithi3 Ogcocephalus cubifrons3 Trichiurus lepturus3
Engraulidae spp.3 Ogcocephalus pantostictus3 Trinectes maculatus3
Enneacanthus gloriosus3 Ogcocephalus radiatus3 Tylosurus crocodilus3
Epinephelus spp.3 Ogyrides alphaerostris3 Tylosurus spp.3
Erotelis smaragdus3 Ogyrides hayi3 Typha latifolia
Etheostoma fusiforme3 Ogyrides sp.3 Typha sp.
Etropus crossotus3 Oligoplites saurus3 Typhaceae
Etropus cyclosquamus3 Ophichthidae3 Unidentified fish3
Etropus microstomus3 Ophichthus gomesii3 Unidentified shrimp3
Etropus spp.3 Ophidion holbrookii3 Urocaris longicaudata3
Eucinostomus argenteus3 Ophidion josephi3 Urophycis floridana3
Eucinostomus gula3 Ophioderma spp. Urophycis regia3
Eucinostomus harengulus3 Ophiothrix (Ophiothrix) angulata Vallisneria americana
Eucinostomus spp.3 Opisthonema oglinum3 Vigna luteola
Eurypanopeus depressus3 Opsanus beta3 Vitta usnea
Eustachys petraea Opsopoeodus emiliae3 Woody debris
Filamentous algae1 Orthopristis chrysoptera3 Xanthidae sp.3
Fimbristylis spadicea Osmundastrum cinnamomeum Xanthidae spp.3
Fowlerichthys radiosus3 Ovalipes floridanus3 Xiphopenaeus kroyeri3
Fundulus grandis3 Ovalipes ocellatus3 Zannichellia palustris
Fundulus similis3 Ovalipes spp.3 Acanthostracion lactrophyrs3
Fundulus spp.3 Pagurus longicarpus3 Acanthostracion quadricornis3

1 - Submerged Aquatic Vegetation, 2 - Coastal Wetlands, 3 - Nekton

References

1.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Apalachicola National Estuarine Research Reserve. Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program. (2024).
2.
Florida Department of Environmental Protection (DEP). Florida STORET / WIN. (2024).
3.
University of Florida (UF); Institute of Food and Agricultural Sciences. Florida LAKEWATCH Program. (2024).
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.
U.S. Environmental Protection Agency (EPA); Office of Research and Development. Environmental Monitoring Assessment Program. (2004).
7.
Florida Fish and Wildlife Conservation Commission (FWC). Fisheries-Independent Monitoring (FIM) Program. (2022).
8.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Apalachicola National Estuarine Research Reserve. Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring. (2023).
9.
Florida Fish and Wildlife Conservation Commission (FWC); Florida Fish and Wildlife Research Institute (FWRI). Harmful Algal Bloom Marine Observation Network. (2018).
10.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Central Panhandle Aquatic Preserves. Central Panhandle Aquatic Preserves Seagrass Monitoring. (2023).
11.
National Oceanic and Atmospheric Administration (NOAA); National Centers for Coastal Ocean Science’s Center for Coastal Monitoring and Assessment. National Status and Trends Bioeffects program. (1994).
12.
Alabama Center for Ecological Resilience (ACER). Oyster shell heights and taxonomic diversity in 2015-2017 among previously documented oiled and non-oiled reefs in Louisiana, Alabama, and the Florida panhandle. (2017).
13.
Oyster Sentinel. Oyster Sentinel . (2016).
14.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Apalachicola National Estuarine Research Reserve. Apalachicola Bay Ephemeral SAV Monitoring. (2004).