Manatees in Jacksonville: Seasons, Survey Counts, Boating Rules and Rescue

Manatees use Jacksonville waters mainly from spring through fall, because when water temperatures drop from December through March most manatees in the lower St. Johns River basin move to warmer South Florida waters (State of the River Report).

For the St. Johns River at Jacksonville the cold limit is physical: the U.S. Fish and Wildlife Service says Florida manatees cannot tolerate water below 68 degrees Fahrenheit for extended periods, and in cooler months many rely on natural springs, power plant outfalls and passive thermal basins (USFWS).

Where they go in Jacksonville matters for boaters and paddlers. The State of the River Report says survey data show manatees feed, rest and mate in greater numbers south of the Fuller Warren Bridge, where their food supply is greatest in Duval County, while sightings in the rest of the county are mostly animals traveling or resting (State of the River Report). Manatees use the Intracoastal Waterway as a travel corridor on their seasonal north and south migrations and stay close to the shore, using small tributaries to feed (State of the River Report).

The report credits those survey results to Jacksonville University, which it says has flown some 798 aerial surveys with over 19,181 manatee sightings from 1994 to 2024, covering the St. Johns River shorelines and tributaries from Jacksonville to Black Creek and the Atlantic Intracoastal Waterway from Nassau Sound to Palm Valley (State of the River Report).

The State of the River Report puts most manatees in the lower St. Johns River basin around Jacksonville, about 260 or more, in the greater Atlantic region subpopulation (State of the River Report).

It also counts a separate group of about 880 from the Blue Springs area whose visits to the basin are not known (State of the River Report).

The report gives an annual mean of 44 manatees per survey in Duval County and adjacent waters for 1994 to 2024, and says reduced sampling after 2012 made it fluctuate more around an 11-year smoothed mean of 43 (State of the River Report). Statewide, the Florida Fish and Wildlife Conservation Commission puts the population at a minimum of 8,350 animals, and the species was reclassified from endangered to threatened under the federal Endangered Species Act in May 2017 (FWC).

The report also notes that state synoptic surveys did not occur in 1993, 1994, 2008, 2012, 2013 and 2020 to 2024 because of unfavorable weather or the COVID-19 pandemic (State of the River Report).

Jacksonville boaters operate under state manatee protection zones for Duval County in Rule 68C-22.027 of the Florida Administrative Code, and the City of Jacksonville (Duval) Manatee Protection Plan that FWC lists with a 2018 revision (FWC Data and Maps; FWC).

The Duval rule, titled Duval County and Associated County (Parts of Clay and St. Johns) Zones, was last amended effective January 30, 2007, and FWC also lists federal manatee protection areas for Duval under 50 CFR 17.108(c)(11) (Florida Administrative Code; FWC).

Duval was one of the 13 key counties that Florida's Governor and Cabinet told to write a Manatee Protection Plan in October 1989, a requirement later written into Florida Statute in 2002 (FWC). The FWC table lists the City of Jacksonville (Duval) plan as approved or last revised in 2018, and FWC and other regulators use these plans when they review permit applications for new or expanding boat facilities (FWC).

The City of Jacksonville page, which now returns an error and survives in a February 2026 archive, described its plan as protection set from an understanding of manatee populations, habitat and human interaction, weighed against recreational and commercial use of the city's waterways, with maps of surveyed locations along the St. Johns River and its tributaries (City of Jacksonville, archived February 7, 2026). The speed zones themselves come from FWC under the Manatee Sanctuary Act, section 379.2431(2), Florida Statutes, and appear in Chapter 68C-22 of the Florida Administrative Code (FWC). A local ordinance can add zones only with FWC approval, and such local zones cannot cover the main marked channel of the Florida Intracoastal Waterway or waters within 100 feet of it (FWC).

Jacksonville Zoo and Gardens advises boaters to stay in deep-water channels whenever possible, follow the speed zones, move slower when in doubt, and avoid boating over seagrass beds and shallow areas, which it calls manatees' most used habitats (Jacksonville Zoo and Gardens).

The State of the River Report says that among lower St. Johns River basin counties, watercraft deaths as a share of each county's manatee mortality were highest in Duval at 29 percent (State of the River Report).

The report tracks Duval County in five-year blocks around 1994, when the interim Duval County protection plan rules took effect. It says Duval watercraft deaths averaged 31 percent of total statewide deaths from 1980 to 2004, rose to 52 percent from 2005 to 2009, then fell to 24 percent of total manatee mortalities in the lower basin for 2010 to 2014 and averaged 16 percent for 2015 to 2019, against an average statewide watercraft death rate of 20 percent for the same period (State of the River Report).

The report calls watercraft-caused mortality the most significant threat to manatee survival, with river traffic that includes port facilities, commercial fishing, sport fishing and recreational boating share the river (State of the River Report). The same report notes Duval and Putnam counties saw a decreasing trend in vessels while St. Johns, Clay and Flagler counties saw an increasing trend (State of the River Report).

An injured, distressed or dead manatee in Jacksonville goes to the FWC Wildlife Alert line at 888-404-3922 (888-404-FWCC), or #FWC or *FWC from a cell phone (FWC).

Jacksonville Zoo and Gardens says it has a Marine Mammal Response Team of zoo staff who help FWC rescue and transport injured marine mammals, and that it built the first-ever Manatee Critical Care Center in Northeast Florida (Jacksonville Zoo and Gardens). The zoo says that before then, any cold-stressed or injured manatee found around the First Coast had to be transported to care centers in Orlando, Tampa or Miami (Jacksonville Zoo).

According to the zoo, the $2.1 million Jacksonville center was funded by private individuals and a $500,000 grant from the State of Florida, and was built to hold 5 to 6 animals at a time until they are healthy enough to return to safe waters (Jacksonville Zoo and Gardens). It sits where the zoo's Education Campus, Wild Florida and the African Forest gorilla exhibit meet, and zoo guests get only limited, periodic views because at times no manatees are in the pools (Jacksonville Zoo).

JEA says winter manatee observations at its facilities have decreased drastically because it built aquatic barriers, aimed at keeping manatees from lingering near its thermal discharge sites along the St. Johns River (JEA).

JEA says it worked with the U.S. Fish and Wildlife Service, FWC and local universities to encourage successful winter migration, and that in winter Northeast Florida manatees head for the warmer waters of the natural spring system (JEA). FWC says the East Coast Unusual Mortality Event from starvation due to seagrass loss, officially dated December 1, 2020 to April 30, 2022 with 1,255 manatee carcasses documented, was administratively closed on March 14, 2025 (FWC).

Some official Jacksonville material is dated. The city's Manatee Protection Plan page still lists a Manatee Implementation Report from 2020 as its newest progress report, and as of October 15, 2026 the live city page returned an error and was readable only in an archived copy from February 7, 2026 (City of Jacksonville, archived February 7, 2026). FWC still lists the 2018 revision as the current Jacksonville plan, and FWC's data and maps page links zone maps for Duval and associated counties (FWC; FWC Data and Maps). Last verified: October 15, 2026, on the FWC website.