The West Indian manatee (which includes both the Florida manatee and Antillean manatee subspecies) is protected by several state and federal acts. As the West Indian manatee is listed as endangered throughout its range, it is protected by the Endangered Species Act of 1973. The Endangered Species Act is administered by the United States Fish and Wildlife Service and National Marine Fisheries Service in cooperation with state agencies. Manatee recovery plans are required under this Act and must include site-specific management activities, measurable criteria, and time estimates for implementing these plans.

As a marine mammal, the West Indian manatee is also protected by the Marine Mammal Protection Act of 1972. This Act protects marine mammals from harassment, injury, molestation, capture, collection, and/or killing. The Marine Mammal Commission administers this Act and has the authority to establish refuges and sanctuaries.

The Florida Manatee Sanctuary Act of 1978 established Florida as a refuge and sanctuary for manatees. The Act protects manatees from injury, disturbance, harassment, or harm in the waters of Florida and allows for enforcement of boat speeds and operations in areas where manatees are concentrated. The Imperiled Species Management Section (ISMS) of the Florida Fish and Wildlife Conservation Commission (FWC) is responsible for coordinating and assisting in the development of these plans.

The Florida Department of Environmental Protection, Florida Marine Patrol, and the Florida Game and Freshwater Fish Commission, that were merged in 1999 under the FWC, are responsible for enforcement.  Conviction under the federal protection acts is punishable by a fine of up to $50,000 and/or one year in prison. The State of Florida can pursue prosecution under federal law in circumstances of extreme harassment, such as severe injury or death to a manatee. Conviction under the state law entails a maximum fine of $500 and/or imprisonment for up to 60 days.