Port of the Islands Marina sits at the threshold of the Ten Thousand Islands, a 35,000-acre labyrinth of mangrove islets where the Faka Union Canal meets the estuarine shallows of Collier County. West Indian manatees — Trichechus manatus latirostris — migrate into these brackish channels each winter when Gulf temperatures drop below 68°F, congregating near warm-water discharges and spring-fed tributaries that buffer them against cold stress. The subspecies, listed as threatened under the Endangered Species Act since 1967 and reclassified from endangered in 2017, depends on shallow coastal corridors for feeding and calving; adult females consume up to 150 pounds of seagrass daily to sustain their 1,200-pound bulk. Guided boat excursions departing from the marina navigate the protected waterways of Fakahatchee Strand Preserve State Park and the western fringe of Everglades National Park, threading between red mangrove prop roots and oyster bars that shelter juvenile tarpon, roseate spoonbills, and nesting ospreys. Manatee eco tour Naples FL operators hold federal permits issued under the Marine Mammal Protection Act, which prohibits pursuit, harassment, and physical contact; captains maintain the mandated 50-foot idle-speed buffer and educate passengers on passive observation protocols. Morning departures between 8:00 and 11:00 capitalize on cooler air temperatures and glassy water — conditions that allow hydrophones to detect manatee vocalizations and increase the likelihood of surface breathing events. The Ten Thousand Islands ecosystem functions as a critical nursery for the Gulf of Mexico's commercial fisheries and a migratory stopover for neotropical songbirds. Sawgrass marshes inland transition abruptly to tidal creeks where salinity fluctuates with the lunar cycle, creating gradients that support both freshwater and marine species within a single tidal basin. Bottlenose dolphins patrol the deeper channels at slack tide, while American crocodiles — the only crocodilian species sympatric with manatees in Florida — bask on mudflats near the park boundary. Naturalist guides interpret the hydrological engineering that defines South Florida's wet season, the role of Hurricane Irma's 2017 storm surge in reshaping barrier islands, and the ongoing federal acquisition of private inholdings to expand the preserve's contiguous acreage. Naples manatee excursions operate year-round, though sightings peak from November through March when aggregations of up to two dozen individuals occupy the warmest pockets of the estuary.