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Florida manatees ( Trichechus manatus latirostris ) are challenged by human alteration of landscapes and waterways. Coastal eutrophication has increased the frequency and intensity of Indian River Lagoon (IRL) algal blooms, promoting seagrass die-offs in areas that once consistently provided manatee forage. For decades the densest aggregations of manatees in Florida, outside of warm-water sites in winter, occurred in the northern Banana River (NBR) at Kennedy Space Center. Historically, the nearby Mosquito Lagoon (ML) had low numbers. Beginning in 2011, several catastrophic algal blooms caused the die-off of nearly 60% of the areal extent of all IRL seagrasses. Most severe impacts were in the Indian River and Banana River with lesser impacts in ML. This study evaluated several decades of manatee aerial survey data using statistical models to identify the environmental and temporal factors influencing manatee abundance, behavior and habitat use in the NBR (1990–2024) and ML (2016–2024). Using a Bayesian hierarchical model, we evaluated how manatee counts were affected by season, water clarity, and coastwide trends in manatee population size. Manatee abundance was evaluated across four distinct IRL seagrass Die-Off periods: Pre-Die-Off, Initial Die-Off (2011-2015), Secondary Die-Off (2016-2022), and Post-Die-Off (2023-2024). NBR manatee abundance increased well into the Initial Die-Off and then declined sharply until reaching historic lows in 2019. Beginning in 2016, only the ML maintained high seagrass coverage and a notable surge in manatee counts indicated aggregations shifted to ML. The Boosted Regression Tree Analysis top two predictors of abundance were seagrass Die-Offs periods and season. Optimized Hotspot Analysis of NBR manatee spatial distribution was compared to seagrass distribution and revealed that during the Pre-Die-Off, manatee hotspots occurred along deep-water resting areas adjacent to seagrass. Starting in the Initial Die-Off, manatee hotspots shifted toward ever shallower waters presumably to access the receding seagrass beds. The proportion of calves observed also declined dramatically after the Initial Die-Off period. These findings demonstrate that manatees aggregate in traditional areas with extreme fidelity but need to shift to “other pastures” during localized seagrass die-offs. Future shifts from habitat degradation will require best practices and adaptive management to safeguard manatees.