CHNEP Clam Habitat Suitability

and Potential Restoration Site Selection

The southern hard clam (Mercenaria campechiensis) and the northern hard clam (M. mercenaria) are both found in the Gulf of Mexico. The southern species is native while the northern species is likely a product of aquaculture introduction. When abundant, hard clams have an important role in estuaries as filter feeders transferring energy throughout the food web. The feeding activity of hard clams reduces phytoplankton and turbidity, which benefits seagrass by increasing water clarity ultimately provides habitat and a food source for marine life. Hard clams are becoming less abundant in most areas of the Gulf of Mexico and resource managers are investigating techniques to effectively restore natural populations along the Florida coast.


Clam Restoration in the Charlotte Harbor Estuary

The hard clam has been harvested by man from the Charlotte Harbor Estuary since at least 300 – 500 AD. Since the mid-twentieth century, over-harvesting, water quality changes, habitat loss and ecosystem disturbance has drastically reduced the abundance of hard clams in Southwest Florida. In fact, the Charlotte Harbor Estuary is a home for clam farm leases in Pine Island and Gasparilla Sounds. Farmers are often faced with an inability to market their clams due to red tide, fishery closures and other natural events. During these instances, the farmed clams are still viable and could be used to help regional restoration efforts by relocating them to suitable areas for their long-term survival and natural propagation.

A Charlotte Harbor Estuary clam restoration study group was formed to address the potential of using unmarketable hard clams for restoration efforts. The study group consists of clam farmers and scientists from Florida Department of Environmental Protection (FDEP), Florida Fish and Wildlife Commission (FWC), and Sanibel Captiva Conservation Foundation (SCCF). The goal of the project was to identify and rank 10 potential clam restoration sites within the Charlotte Harbor Estuary which provide optimum habitat suitability with minimal logistical challenges.

Suitability Map

This interactive map shows combined suitability factors with aggregated suitability scores for each pixel. The dark green areas indicate predicted most suitable habitat while the red areas predict unsuitable habitat. This map will be used to survey potential clam restoration sites located within habitat predicted to be suitable.


By examining the findings of previous studies, the environmental characteristics needed for successful hard clam growth and survival were identified (Table 1). Environmental factors including sediment, salinity, temperature, dissolved oxygen, chlorophyll a, seagrass cover, currents, depth and existing clam density help to identify appropriate locations for clam placement. Analysis of existing environmental data for the Charlotte Harbor estuary using ArcGIS tools provided comparisons of current conditions to desired optimal conditions. A GIS-based model was then developed which identifies areas that should provide the best habitat for hard clams.

Table 1. Factors used in GIS habitat suitability map development.

Factor Optimal Acceptable Marginal Unsuitable Exposure Duration Notes
Salinity, psu >25 20–25 12.5–20 <12.5 or >45 3–6 days of unsuitable  
Seagrass coverage 0% <10% 10–25% seagrass with sandy mud to shelly mud substrate No seagrass with anoxic, unconsolidated mud or abundant seagrass   Greater food availability with seagrass present but state and federal permitting concerns
Flow or food flux Flowrates from 0.2–0.6 cm/sec for densities of 4–450 clams/m2     Greater flow increases food delivery
Substrate Shelly soft bottoms Sandy to Muddy Sand Sandy Mud Unconsolidated muddy bottoms – Anoxic    
Chlorophyll a, μg/l Seston flux is best indicator of growth = optimum seston flux = 90–130 mg/cm2-sec POM anything greater than or less than optimum may reduce growth. Chlorophyll a is measure of phytoplankton (food)
Harvesting area No harvesting permitted Conditional harvesting permitted Harvesting permitted     Areas where harvesting is permitted may increase poaching of restored clams
Depth meters 4–8 6–18 0–3, 18–30 >30    
Dissolved oxygen, mg/l >5 4.2–5.0 2–4.2 <1    
Temperature, °C 22.5–30 12.5–30 30–31 >32 Can survive 32°C for 15 days w/o mortality at 25 ppt  

The data, within a series of Geographic Information System (GIS) layers, was scored for suitability on a scale 0 to 3, with 3 being most suitable or optimal habitat. Draft clam habitat suitability maps were developed using this scoring procedure and color coding on the GIS map layers. The composite suitability maps were then used to identify sites for exploratory field surveys of actual conditions in areas which are both suitable and accessible. Green is optimal, light green acceptable, yellow marginal and red unsuitable. Scores for each suitability class:

  • Optimal = 3
  • Acceptable = 2
  • Marginal = 1
  • Unsuitable = 0

Unsuitable areas for dissolved oxygen, temperature and salinity were mapped and shown in red for final composite map. These are areas not to be considered for clam relocation.

Based on the map, logistical factors, and discussions with local stakeholders, 10 potential restoration sites were selected and surveyed for the presence of hard clams. The field studies provided the information needed to rank the 10 potential restoration sites relative to one another. The factors included adult clam density, juvenile clam density, seagrass coverage, bottom substrate percent silt, estimated relative food flux (relative flow rate × mean chlorophyll a), and presence of shell in the substrate. Each factor was scored on a 0–3 scale (0 being worst, 3 being best).

Table 2. Factor values and associated scores for site suitability in this study

Factor Optimal Score (3) Acceptable (2) Marginal (1) Unsuitable (0)
Mean Number Adult Clams/m2 1–5 5–10 0 >10
Mean Number Juvenile Clams/m2 >100 10–100 0–10 0
Mean % Silt <10% 10%–15% 15%–20% >20%
Seagrass Cover % 0% 1%–10% 10%–25% >25%
Shelly Substrate Presence Very Shelly Shelly Some Shells Not Shelly
Relative Food Flux (This Score Doubled) >9 6–9 3–6 0–3

Suitability Summary

Adult hard clams were found at three of the sites at low densities. These three sites with adult clams present were ranked as best potential sites. Based upon the information collected in our field surveys and through the GIS-based habitat suitability analysis, four sites are recommended for further consideration as initial clam restoration sites (Figure 19, Table 3). Three of the sites (sites CR11, CR19, and CR17) have adult clams in low concentrations while the fourth (site CR15) has high relative food flux, no seagrass cover, and sandy-shelly substrate. Site CR17 is located north of Sandfly Key in Gasparilla Sound. Site 19 is located near Grouper Hole in Gasparilla Sound. Site CR11 is located west of MacKeever Keys in Pine Island Sound, and site CR15 is in Charlotte Harbor just south of Turtle Bay. All sites are located in 6-8 feet of water, have salinity and oxygen regimes suitable for clam survival, and little or no seagrass. These sites also provide nearby choices for farmers working leases in Pine Island Sound, Gasparilla Sound or the Charlotte Harbor area. Although other sites surveyed during this study were ranked lower in the analysis, any of them except site CR9 near York Island would potentially support a clam population.

Table 3. Recommended Restoration Sites

Site ID Site Description Latitude Longitude Rank Waterbody
CR11 Pine Island Sound West McKever Keys 26.51422985870 -82.12506125710 1 Pine Island Sound
CR19 Grouper Hole off Boca Grande 26.79385540200 -82.26451181090 2 Gasparilla Sound
CR17 North Sandfly Key 26.78959671370 -82.24588205720 3 Gasparilla Sound
CR15 CH at Southern Mouth Turtle Bay 26.77915158590 -82.16569241180 4 Charlotte Harbor
CR14 Pine Island Sound West Demere Key Near Clam Leases 26.59334017870 -82.15758863240 5 Pine Island Sound
CR12 CH N of Bokeelia S of Jug Creek Point Shoal 26.70623211270 -82.13270706030 6 Charlotte Harbor
CR18 South of Placida 26.81429562470 -82.25313409460 7 Gasparilla Sound
CR13 Pine Island Sound North Chino Island West McKever 26.51465703390 -82.13393090260 8 Pine Island Sound
CR16 Pine Island Sound NE Buck Key Near Bar 26.52673100600 -82.16817702250 9 Pine Island Sound
CR16 Pine Island Sound SW of York Island 26.48399951960 -82.10842993270 10 Pine Island Sound

Now, SCCF is in the process of collaborating with local conservation groups to share our research and develop a statewide plan guiding restoration practices and projects.

Related Links

Hard Clam Habitat Suitability Model and Potential Restoration Site Selection – Project Award CZ226-A1, SCCF Marine Laboratory, by Mark Thompson, Eric Milbrandt, and Leah Reidenbach, January 31, 2021

Project Contacts


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