Abstract Nearly half of Earth’s seasonal freshwater storage variability occurs in human‐managed reservoirs, resulting in large areas of reservoir‐bed that are episodically inundated or subaerially exposed. Here we use hyperspectral data from NASA’s Earth Surface Mineral Dust Source Investigation (EMIT) mission to map calcite mineral assemblages across exposed surfaces in two large U.S. reservoirs, Lake Mead and Lake Powell. Results show distinct patterns in the occurrence of carbonate, clay, and mica minerals. Reservoir‐deposited sediments exhibited significantly higher calcite proportions than adjacent, lithologically similar, non‐inundated terrestrial surfaces. These differences likely reflect hydrologically‐driven calcite precipitation, wherein warm, clear, productive reservoir waters drive calcium carbonate out of solution. We also detect reductions in calcite proportions in areas of the shoreline disturbed by human recreation. EMIT’s imaging capabilities enable rapid, high‐resolution mineralogical inventories across vast areas where field sampling is infeasible. We find EMIT is a scalable tool for monitoring geochemical changes associated with large water level fluctuations.