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The Coongie Lakes are a series of ephemeral freshwater lakes on the lower reaches of Cooper Creek, a large intermittent river of the arid Lake Eyre Basin, Australia. Hydrogeological, chemical, and isotopic observations, in conjunction with numerical modeling of groundwater responses to lake inundation events, have been used to identify the dominant processes linking shallow, unconfined groundwater with the hydrology of the lakes during wet and dry periods. The lakes are predominantly zones of net groundwater recharge during inundation events. However, soil profile data suggests that drying of some of these lakes allows evaporative groundwater discharge to occur through the soil profile of the dry lake beds, resulting in salinization of the soil profile of the more ephemeral lakes. The occurrence of young, high-salinity groundwater is best explained by variations in soil profile flushing in response to wet and dry interannual periods of river discharge. During interannual drier phases, when filling of previously dry lakes is more common, recharge is mostly via macropore flow during the rising stage of the inundation. Increased salinization of the lake-bed sediments occurs during longer dry periods due to transport of solutes to the near-surface from lake-bed evaporation and limited flushing of the soil profile because of the macropore-dominated flow during recharge. During wet periods, recharge is more likely dominated by matrix flow that results in leaching of the soil profile and increased export of solutes into the alluvial aquifer.