Stable isotopes of oxygen and hydrogen are used here with salinity data in geochemical and mass-balance models to decipher the proportion of different sources of water in two hypersaline estuaries that vary in size and hydrologic condition. Shark Bay, located on the mid-western coast of Australia, is hypersaline year round and has an arid climate. Florida Bay, located in the south-eastern United States, is seasonally hypersaline and has a subtropical climate. The water budget in both bays can be explained by evaporation of seawater, with seasonal inputs of surface-water runoff and precipitation. In Shark Bay, discharge from the Wooramel River associated with a recent major flood was detected in the relationship between the stable isotopic composition and salinity of surface waters near the mouth of the river, despite the persistence of hypersalinity. The volume of water equal to one pool volume replenished Hamelin Pool (a hypersaline water body located at the southern end of eastern Shark Bay that supports living stromatolites) once every 6–12 months. The eastern portion of Florida Bay received a greater proportion of freshwater from overland flow (70–80%) than did the western portion where rainfall was the dominant source of freshwater.