Background: Description of Alligator Harbor

• Located in eastern Franklin 

County; Nearby towns or cities -

Alligator Point, St. Theresa, Turkey 

Point, Lanark Village 

• Lies just east of the Apalachicola 

estuary

• Surface water area of the entire 

preserve is approximately 14,366; 

4,045 acre harbor

• Along with being designated an 

aquatic preserve (1969) is also an 

Outstanding Florida Waterbody, 

Class II Shellfish Harvesting water 

body and EPA Gulf of Mexico 

Ecological Management Site (GEM) 
Watershed

• Apalachicola-Chattahoochee-Flint 

The basin drains an area of more than 

19,300 square miles (50,000 km2).
•Harbor is approximately 4 1⁄2 miles long and 1 1⁄2 

miles wide with a mean water depth of ~4 feet. The 

western end of the harbor, connecting with the 

Gulf, is almost closed by a shallow sandbar except 

for a deeper channel on the northern end. 

•Depths at the harbor mouth are about 8-10 feet 

(Yentsch, 1953). Depths from the harbor mouth to 

western boundaries of AP boundaries range 

between 4 to 17 feet. 

•Shallow, neutral bay with no significant freshwater 

inflow and relatively stable salinities.

•Salinities in the area range from 30-35 ppt; 

essentially the same as the Gulf 

•Characteristics are due in part to extremely small 

drainage basin and to regular tidal exchange with 

the water of Apalachicola Bay. 

•Only during extremely heavy rains can any 

appreciable amount of freshwater enter the harbor. 

Background: Description of Alligator Harbor
• Domestic Wastewater Treatment Plant 

Systems- 1 WWTP in the shoreline areaSummer Camp WWTP is not currently in 

operation- will become operational when the 

Summer Camp Development has a community 

of 50 residents; KOA WWTP was removed in 

March 2006

• Marinas- Alligator Point Marina- 45 boats, 

restrooms, fueling, mean depth 8.5, has 

required buffer zones.

• Stormwater- All stormwater enters the 

system via rainfall driven runoff and has the 

potential to affect the area- mainly from the 

developed southern shoreline.

•Agricultural waste- No domestic animal farms 

in the harvesting area

• Industrial waste- No permitted sources of 

industrial waste

• Septic systems- 118 (indirect- the property 

serviced by the septic system is within 100 feet 

of the shoreline of the shellfish harvesting 

area)

Actual/Potential Pollution Sources
Water Quality Monitoring- Dataloggers

• Monitoring eastern AH 2007-2008

• Continuous data- 30 minute intervals; sonde 

retrieved/deployed every 2 weeks

•Parameters include- dissolved oxygen, 

salinity, temperature, turbidity, pH

• Current state of water quality in eastern 

portion of harbor

*

FDACS
Datalogger Water Quality Data 10/2007-8/2008 Daily Averages

• Water temperatures range from 5.8-31.1°C with peak temperatures generally occurring in July/August and lowest 

temperatures occurring in December and January

• pH in the harbor averages 8.0

• Dissolved oxygen (DO) varied from 40-100% +saturation; peak levels occurring in the winter and spring and lower levels 

occurring in the summer and fall when temperatures are higher

• Salinity values ranged from 28-38 ppt with an average of 34 ppt

• Turbidity values typically range from 0-264 NTU’s ; higher values are usually associated with storm events

• Average depth in eastern harbor is 3.5 feet 
Site Specific Summaries by Station

• YSI 85 hand-held unit on a monthly basis at each location (plus scallop spat monitoring 

stations-11) for DO, salinity, pH, temperature (2006-2009)

AHCW1– Ave pH is 8; Ave Salinity 31.3ppt; 

Ave DO 90% (s)
Water Quality Monitoring- Nutrients

• AP monitors 7 sites on a monthly basis - since 2001

• Partnership through the University of Florida’s LAKEWATCH/Coastwatch program- total nitrogen, total phosphorus, chlorophyll and clarity
Average TN: 247-495 μg/L 

Average Chlorophyll: 2-9 μg/L

Average TP: 13-41 μg/L 

Alligator Harbor Aquatic Preserve Monthly Nutrient Monitoring 

Site Specific Annual Averages 2001-2009

Valued Biological Resources- Seagrass

• Monitoring specific stations using fixed transects and random point sampling methods: 2002-2009

• 7 stations (4 quads) = 28 locations

• Data collected- seagrass/algae species present, percent coverage using Braun Blaquet method, blade 

lengths, depth, classify epiphyte coverage (clean, light, medium, heavy), sediment type, other organisms 

present, photosynthetic active radiation (PAR)- amt. of light reaching the bed... LAB- collect 3 shoots for 

epiphyte weight (g), 4 cores to determine above/below ground biomass, sediment sample for grain-size 

analysis, turbidity sample.....• Map each location- using GeoXT Trimble unit
• Historical seagrass coverage from 1995 FWRI layer indicate there are 3,661 acres of 

seagrass habitat within the Alligator Harbor Aquatic Preserve boundaries.

• Preserve staff are currently mapping seagrass habitat from 2007 DOQQ imagery 

(Dept. of Revenue) to determine extent of habitat



Valued Biological Resources- Clam Aquaculture Leases

• Established in 2002 

• 40 leases implemented; ~10 of these are being cultivated

• Resulting in small product; those still active are producing a valuable product

• AHAP is a great growing area due to high salinity and good water quality

• Values of this resource have dropped due to reduced demand; decrease in production seen; 

but is still new and growing- takes a 10-year period to determine success

• FDACS monitors 20 bacteriological water quality-sampling stations in the harbor; datalogger at 

clam site
Alligator Harbor Data Sonde FDACS- Live Water Monitoring

http://sondes.floridaaquaculture.com/sondes/sonde_maphome.htm

*
Historical Research & Data: Publications

FSU Marine Lab 

Revision of Alligator Harbor Management Plan

• Current version 1986

• Discussing site-specific management issues and pulling together historical data, monitoring 

data, etc. 

• 2011/2012