The projected effects of climate change include an increase in the frequency and intensity of storm events and sea‐level rise, which can erode and degrade coastal habitats and affect coastal‐dependent species. The American oystercatcher (Haematopus palliatus) is a shorebird that is dependent on low‐lying coastal habitats for breeding and wintering and is particularly vulnerable to the effects of climate change and sea‐level rise. We investigated the degree to which changes in duration of flooding of roosts affected annual survival of individuals in a large wintering population of oystercatchers on the Nature Coast of Florida, USA. We used 12 years (2007–2018) of mark‐resight data from a large‐scale monitoring effort that included winter resights on Florida's Nature Coast to model the annual survival and site fidelity of sub‐adult and adult birds. High‐tide roosts are limited in number and are a potential population‐limiting factor for wintering oystercatchers. We assessed the effect of roost inundation on survival and site fidelity by incorporating the number of hours roosts were at risk of inundation during extreme higher high tide events each winter. We documented a 7.3% decline in annual survival, from 0.96 to 0.89, over the study period, and survival rates did not differ between age stages. The decline was associated with an increase in the duration of extreme higher high tides, which had a negative effect (β = −0.003; 95% CI = −0.006 to −0.001) on survival. Site fidelity varied across the study period and among age stages, with lower rates in sub‐adults (0.85; 95% CI = 0.80–0.89) than in adults (0.94; 95% CI = 0.89–0.97). The duration of nest and roost inundation are among the greatest threats to oystercatcher populations, and high‐tide roosts are an important habitat component for wintering populations on the Nature Coast. Sea‐level rise is predicted to increase, which will contribute to the increasing inundation duration of coastal habitats. Our results underscore the importance of conservation and restoration of important wintering habitats to mitigate threats to the population viability of oystercatchers in Florida and throughout their range.