Authigenic calcite silts at Wadi Midauwara in Kharga Oasis, Egypt, indicate the prolonged presence of surface water during the Marine Isotope Stage 5e pluvial phase recognized across North Africa. Exposed over an area of ∼ 4.25 km2, these silts record the ponding of water derived from springs along the Libyan Plateau escarpment and from surface drainage. The δ18O values of these lacustrine carbonates (− 11.3‰ to − 8.0‰ PDB), are too high to reflect equilibrium precipitation with Nubian aquifer water or water of an exclusively Atlantic origin. Mg/Ca and Sr/Ca of the silts have a modest negative covariance with silt δ18O values, suggesting that the water may have experienced the shortest residence time in local aquifers when the water δ18O values were highest. Furthermore, intra-shell δ18O, Sr/Ca, and Ba/Ca analyses of the freshwater gastropod Melanoides tuberculata are consistent with a perennially fresh water source, suggesting that strong evaporative effects expected in a monsoonal climate did not occur, or that dry season spring flow was of sufficient magnitude to mute the effects of evaporation. The input of a second, isotopically heavier water source to aquifers, possibly Indian Ocean monsoonal rain, could explain the observed trends in δ18O and minor element ratios.