Here, we focus on Ambaro and Ambanja bays, presenting dynamics calculated using United States Geological Survey (USGS) national-level mangrove maps and the first localized satellite imagery derived map of dominant land-cover types. The analysis of USGS data indicated a loss of 7659 ha (23.7%) and a gain of 995 ha (3.1%) from 1990–2010. Contemporary mapping results were 93.4% accurate overall (Kappa 0.9), with producer’s and user’s accuracies ≥85%. Classification results allowed partitioning mangroves in to ecologically meaningful, spectrally distinct strata, wherein field measurements facilitated estimating the first total carbon stocks for mangroves in Madagascar.