A decline in submerged aquatic vegetation (SAV) within Florida’s spring-fed thermal refuges raises questions about how these systems support winter foraging of Florida manatees Trichechus manatus latirostris. We analyzed telemetry data for 12 manatees over 7 yr to assess their use of Kings Bay, a winter refuge with diminished SAV. After accounting for the effect of water temperature, we hypothesized that the number of trips out of Kings Bay would increase and the time wintering manatees spent in Kings Bay would decrease. Trips out of and into Kings Bay were also compared to assess potential influences on exiting or entering. There were no detectable differences in the number of trips out of the bay or overall time manatees spent in Kings Bay across winters. The percentage of time water temperatures were below 20°C was the single best predictor of increased time spent in Kings Bay. Trips out of Kings Bay were more likely than trips into the bay to occur after 12:00 h and during a high but ebbing tide. Nine manatees tracked for longer than 75 d in winter spent 7 to 57% of their time in the Gulf of Mexico, and 3 of these manatees spent 7 to 65% of the winter >80 km from the mouth of Kings Bay. Results suggest the low amount of SAV in Kings Bay does not obviate its use by manatees, though there are likely tradeoffs for manatees regularly foraging elsewhere. Accounting for movements of Florida manatees through a network of habitats may improve management strategies and facilitate desirable conservation outcomes.