Mollusk reefs, perhaps the most impacted natural habitat type in CHAP, are expansive concentrations of sessile mollusks (usually the Eastern oyster in Florida) occurring in intertidal and subtidal zones to a depth of 40 feet and are typically referred to as oyster reefs or oyster beds. Oyster reef habitat provides numerous ecosystem services: They are essential fish habitat, bio-assimilate nutrients, filter water, reduce turbidity and stabilize shorelines, among numerous other functions. Tolley, Volety, and Savarese (2005) studied the resident communities of oyster reefs in the Caloosahatchee estuary and identified ten species of decapods and 16 species of fish living on the oyster reef. At least 90 percent of oyster reef habitat in the Charlotte Harbor region is estimated to have been lost as a result of dredging, mining for road beds, hydrologic changes, and harvest (Boswell, Ott, Birch, & Cobb, 2012). Natural predators impacting mollusk reefs within CHAP include stone crabs, blue crabs, oyster drills (Stramonita haemastoma), sheepshead (Archosargus probatocephalus), black drum (Pogonias cromis) and other fishes and invertebrates. The relative abundance (0.1 percent) of the oyster reef is low throughout CHAP. Lemon Bay and Cape Haze aquatic preserves have a slightly higher percentage (0.2 percent) of oyster reefs than the other aquatic preserves.

In partnership with many regional stakeholders, restoring oyster habitat is an important goal within the aquatic preserves and the adjacent waters. A pilot oyster creation project was initiated in the Peace River, called Trabue, by The Nature Conservancy, Charlotte Harbor National Estuary Program, City of Punta Gorda, and many local volunteers. Oyster bags and mats were made by volunteers, and were installed along with the loose shell. To date, the oyster bags have been the most successful in recruiting new oysters. Over 1,300 volunteers contributed to the success of this project, and they continue to monitor the success of the new oyster reefs.