Cockroach Bay Aquatic Preserve was designated in 1976. Of the four aquatic preserves in the Tampa Bay region, it is the least developed and is in the most pristine condition. Portions of the submerged lands within the preserve are not state-owned, but leased from the Tampa Port Authority.

The preserve begins in the mouth of the Little Manatee River, including the river to US 301, and continues southwest past Cockroach Bay to the Manatee County line, extending 2,000 feet from the shoreline. It surrounds several mangrove islands, most of which are state-owned, and borders the Little Manatee River State Park. There is extensive mosquito ditching in some portions of Cockroach Bay and some canals along the Little Manatee River, buth otherwise, the surrounding lands remain in a natural state.