Manatees of the St. Johns — Jacksonville, Florida

The West Indian manatee (Trichechus manatus latirostris) is among the federally listed threatened and endangered species documented in the Lower St. Johns River Basin, alongside the bald eagle, wood stork, and shortnose sturgeon, all protected under the Endangered Species Act of 1973. The St. Johns River — one of the few major rivers in North America that flows northward — bisects Jacksonville's urban core before turning east toward the Atlantic Ocean, and the University of North Florida's State of the River Report documents the river as habitat for two distinct manatee subpopulations. The river's humid subtropical climate, navigable tributaries, and historically abundant submerged aquatic vegetation have made it a year-round and seasonal corridor for manatees moving between inland wintering areas and the Atlantic coast.

Jacksonville's consolidated city-county government, along with state and federal agencies, manages manatee protection through a layered framework that includes the city's own state-approved Manatee Protection Plan, aerial research programs at Jacksonville University, a critical care rehabilitation facility at Jacksonville Zoo and Gardens, and utility infrastructure measures by JEA. The U.S. Fish and Wildlife Service has estimated the total Florida manatee population at fewer than 8,400 animals, according to Jacksonville Today (April 25, 2025), placing the river's resident and migratory animals within a population that commands significant conservation attention at the local, state, and federal levels.

The UNF State of the River Report identifies two manatee subpopulations using the Lower St. Johns River Basin. The larger group — approximately 880 animals — is associated with the Blue Springs area in Volusia County upstream, where a natural thermal spring draws manatees during cold months. A second, resident Atlantic coast subpopulation of approximately 260 animals uses the lower basin more directly, including stretches of the St. Johns River that pass through Jacksonville proper.

Submerged aquatic vegetation (SAV) is the primary food source sustaining these animals in the river. The St. Johns Riverkeeper, an environmental nonprofit conducting river stewardship and public education work, documents manatee presence in the St. Johns year-round and identifies SAV degradation as a central habitat threat. Seagrass and other aquatic grasses in the Lower St. Johns River Basin have not recovered to pre-2017 levels following storm impacts in that year, according to Jacksonville Today (April 2025).

The river's role as a migratory corridor is tied to Jacksonville's climate: manatees seek warmer inland waters during colder months and disperse into coastal and offshore areas as water temperatures rise. JEA's thermal discharge sites along the St. Johns River represent artificial heat sources that can attract manatees in winter, a dynamic that the utility actively manages through aquatic barrier installations.

In October 1989, Florida's Governor and Cabinet directed 13 counties identified as having elevated watercraft-related manatee mortality — including Duval County — to develop local Manatee Protection Plans (MPPs). The requirement was subsequently codified in Florida statute in 2002, according to the Florida Fish and Wildlife Conservation Commission. MPPs serve a regulatory function: they are used by state permitting agencies when evaluating applications for new or expanded watercraft facilities such as marinas and boat ramps.

The Jacksonville City Council adopted the fourth revision of the Duval County Manatee Protection Plan on February 13, 2018, according to the UNF State of the River Report. The plan, administered through the City of Jacksonville's Parks and Recreation department, governs boating speed zones across the St. Johns River and its tributaries within Duval County, as described by Jacksonville.gov. Speed zone designations — including idle speed, slow speed, and minimum wake areas — are established based on manatee habitat surveys and documented animal presence patterns in specific river segments.

The FWC holds the state-level authority over Manatee Protection Plans, and the city's plan must remain consistent with state standards. Jacksonville's consolidated government structure means the city-county entity carries unified responsibility for implementing and updating the plan, a governance arrangement that distinguishes Jacksonville from counties where city and county planning functions operate separately.

Jacksonville University's Marine Science Research Institute operates one of the longest continuous manatee aerial survey programs in the Lower St. Johns River Basin. From 1994 through 2024, the program conducted 798 aerial surveys and recorded 19,181 manatee sightings, according to the UNF State of the River Report. This three-decade dataset provides a longitudinal record of population distribution, seasonal movement patterns, and habitat use across the basin's navigable waterways.

In April 2025, Jacksonville University hosted a multi-stakeholder committee convened by the Public Trust for Conservation to address the intersection of manatee-watercraft collisions and habitat loss. Jacksonville Today reported that JU Associate Professor Ashley Johnson presented mapping work at the meeting, documenting the spatial relationship between boat traffic patterns and areas of known manatee concentration. The committee included representatives from conservation, regulatory, educational, and maritime commerce sectors, and its work focused on developing awareness protocols for commercial shipping operations as well as long-term SAV restoration strategies.

The St. Johns Riverkeeper also conducts research on submerged aquatic vegetation distribution as part of its habitat stewardship mission, with SAV mapping directly informing understanding of where manatee foraging is concentrated in the river system.

Jacksonville Zoo and Gardens operates the J. Wayne and Delores Barr Weaver Manatee River, a 330,000-gallon critical care facility capable of housing up to 20 manatees simultaneously for rescue, rehabilitation, and preparation for release, according to the Zoo's Florida Manatee page. The facility is described as the only Manatee Critical Care Center in Northeast Florida, per the Zoo's Manatee Rescue and Rehabilitation page.

The Zoo operates a Marine Mammal Response Team and is a member of the Manatee Rescue and Rehabilitation Partnership (MRP), a national network of facilities coordinated in part by federal wildlife agencies. The Zoo partners with the Florida Fish and Wildlife Conservation Commission to respond to cold-stressed and injured manatees throughout Northeast Florida, handling rescue logistics, transportation, and clinical care before animals are cleared for return to natural habitat. Cold-stress syndrome — in which manatees experience immune compromise and organ failure when water temperatures fall below tolerable thresholds — is a documented mortality driver for the species, and Jacksonville's position at the southern end of the animals' northeastern range places the Zoo's facility at a geographically significant point in the regional rescue network.

Watercraft strikes are among the leading documented causes of manatee mortality in Florida. The Florida Fish and Wildlife Conservation Commission recorded 565 manatee deaths statewide in 2024, with approximately one-quarter of those fatalities attributed to watercraft strikes, according to Jacksonville Today (April 25, 2025). The St. Johns River's dual role as a working maritime corridor — serving JAXPORT's commercial shipping traffic as well as substantial recreational boating — creates conditions in which manatees share navigable water with vessels ranging from large container ships to personal watercraft.

A 2023 incident illustrated the severity of that overlap: a commercial shipping vessel struck a mating herd on the St. Johns River, killing five manatees, according to Jacksonville Today. That incident accelerated stakeholder engagement around commercial vessel awareness protocols in the river. At the April 2025 committee meeting at Jacksonville University, Gerard Pinto provided documented commentary on trends in recreational boat strikes, reinforcing that recreational watercraft — not only commercial shipping — represent an ongoing collision threat.

Habitat degradation compounds the mortality risk. Submerged aquatic vegetation in the Lower St. Johns River Basin has not recovered since storm-related damage in 2017, as reported by Jacksonville Today. SAV loss reduces the food supply available to manatees using the river, potentially affecting animal body condition and resilience. The St. Johns Riverkeeper identifies SAV restoration as a central conservation priority, with the nonprofit's research connecting grass bed health directly to the river's capacity to support the manatee population documented in aerial surveys since 1994.

Manatee protection on the St. Johns River in Jacksonville involves a layered set of institutions operating at local, state, and federal levels. The City of Jacksonville, through its consolidated government, administers the Duval County Manatee Protection Plan and carries the responsibility — originating in a 1989 state directive — of maintaining boating speed regulations keyed to documented manatee habitat in the river. The Florida Fish and Wildlife Conservation Commission holds state oversight authority, including enforcement of speed zones and coordination of rescue responses.

At the federal level, the U.S. Fish and Wildlife Service maintains jurisdiction over the West Indian manatee under the Endangered Species Act of 1973 and sets population-level management standards that inform local planning. JEA, the city's community-owned utility serving approximately 524,378 electric customers, has installed aquatic barriers at its thermal discharge sites on the St. Johns River to discourage manatees from congregating near artificial heat sources in winter, collaborating with USFWS, FWC, and local universities in that effort, according to JEA's Wildlife Protection page.

The Public Trust for Conservation convened the April 2025 multi-stakeholder committee at Jacksonville University, bringing together the conservation, regulatory, academic, and maritime commerce communities to coordinate responses to both collision risk and habitat degradation. Jacksonville University's Marine Science Research Institute, the St. Johns Riverkeeper, Jacksonville Zoo and Gardens, FWC, and USFWS are all documented participants in this institutional ecosystem. Together, these entities form the operational network through which manatee monitoring, protection plan enforcement, rescue, rehabilitation, and long-term habitat restoration are pursued in the Lower St. Johns River Basin.