Jensen Beach to Jupiter Inlet Aquatic Preserve is part of southeast Florida's Indian River Lagoon (IRL). The Indian River Lagoon is an extensive ecosystem spanning two biogeographic zones characterized by diverse land and water body formations. It possesses wide shallow lagoons and narrow tidal creeks. The lagoon is bordered mostly by intertidal mangrove fringes and salt marshes that are periodically sectioned by man-made mosquito impoundments and residential development. Much of its open waters are dotted by oyster bars, clam beds and spoil islands. The submerged lands are a mosaic of seagrass and algae beds, bare sandy areas, and deep water sites. All of these features combine to create the most diverse (species-rich) and productive estuary in North America.

Recreational uses include fishing, boating, and swimming. Agriculture and residential communities use connecting canals for drainage. Mangroves, leatherfern, sawgrass, tidal marsh and floodplain forest make up the primary plant communities along the riverfront. The aquatic preserve contains fishes, turtles, birds, alligators, and manatees. The adjacent Savannas Preserve State Park contains various natural communities such as pine flatwoods and scrub.