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 portions of the platform. The most chemically evolved groundwater occurs at the end of the longest and deepest flow paths, which discharge near the center of the platform because of incision of the Santa Fe River at the edge of the confining unit. This pattern of discharge of mineralized water differs from fully confined or unconfined platforms where discharge of the most mineralized water occurs at the coast. Mineralized water flowing into the Santa Fe River is diluted by less evolved water derived from shorter, shallower flow paths that discharge to the river downstream. Formation of rivers shortens flow path lengths, thereby decreasing groundwater residence times and allowing freshwater to discharge more quickly to the oceans in the newly formed rivers than in platforms that lack rivers. Similar dynamic changes to groundwater systems should be expected to occur in the future as climate change and sea level rise develop surface water on other carbonate platforms and low lying coastal aquifer systems. Copyright © 2012 John Wiley & Sons, Ltd.