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Much of what is known about groundwater circulation and geochemical evolution in carbonate platforms is based on platforms that are fully confined or unconfined. Much less is known about groundwater flow paths and geochemical evolution in partially confined platforms, particularly those supporting surface water. In north‐central Florida, sea level rise and a transition to a wetter climate during the Holocene formed rivers in unconfined portions of the Florida carbonate platform. Focusing on data from the Santa Fe River basin, we show river formation has led to important differences in the hydrological and geochemical evolution of the Santa Fe River basin relative to fully confined or unconfined platforms. Runoff from the siliciclastic confining layer drove river incision and created topographic relief, reorienting the termination of local and regional groundwater flow paths from the coast to the rivers in unconfined …