Mangrove forests, one of the world's most endangered ecosystems, are also some of the most difficult to access. This is especially true along the Pacific coast of Costa Rica, where 99% of the country's mangroves occur. Unmanned Aerial Systems (UAS), or drones, have become a convenient tool for natural area assessment, and offer a solution to the problems of remote mangrove monitoring. This study is the first to use UAS to analyze the structure of a mangrove forests within Central America. Our goals were to (1) determine the forest structure of two estuaries in northwestern Costa Rica through traditional ground measurements, (2) assess the accuracy of UAS measurements of canopy height and percent coverage and (3) determine whether the normalized difference vegetation index (NDVI) could discriminate between the most abundant mangrove species. We flew a UAS equipped with a single NDVI sensor during the peak wet (Sept-Nov) and dry (Jan-Feb) seasons. The structure and species composition of the estuaries showed a possible transition between the wet mangroves of southern Costa Rica and the drier northern mangroves. UAS-derived measurements at 100 cm/pixel resolution of percent canopy coverage and maximum and mean canopy height were not statistically different from ground measurements (p > 0.05). However, there were differences in mean canopy height at 10 cm/pixel resolution (p = 0.043), indicating diminished returns in accuracy as resolution becomes extremely fine. Mean NDVI values of Avicennia germinans (most abundant species) changed significantly between seasons (p < 0.001). Mean NDVI of Rhizophora racemosa (second most abundant species) was significantly different from A. germinans and dry forest dominant plots during the dry season (p < 0.001), demonstrating NDVI's capability of discriminating mangrove species. This study provides the first structural assessment of the studied estuaries and a framework for future studies of mangroves using UAS.