Coastal beach ecosystems support critical habitat for numerous species and are vulnerable to sea level rise. Sand beaches are spatially and temporally dynamic, making it difficult to accurately predict future habitat loss – estimates that are crucial as species are being assessed for protection. We mapped sand beach habitat on 12 focal barrier islands and low-lying beaches off the Gulf Coast of Florida, USA using two methods for comparison - a remotely sensed land cover and hand-digitized aerial imagery that was collected concurrently with digital elevation data. We then compared estimates of beach habitat lost to sea level rise between the two methods and compared this sensitivity to control mangrove islands. Predictions suggest that most of the beach habitat in our study areas will be underwater within the next century. These beaches represent critical nesting habitat for vulnerable vertebrate species such as the snowy plover (Charadrius nivosus) and the loggerhead turtle (Caretta caretta). Importantly, we found that for some islands, using remotely sensed land cover data led us to under- or over-estimate the amount of beach habitat lost to sea level rise relative to the digitized data because of the temporal mismatch between land cover and elevation data. In contrast, we found relatively little difference between methods in the amount of mangrove forest lost to sea level rise on nearby control islands. We suggest that using land cover data collected at the same time as elevation data can produce more accurate predictions of beach habitat inundation from sea level rise.