Most conceptual models of epigenic conduit development assume that conduits sourcing karst springs form as water that is undersaturated with respect to carbonate minerals flows from recharge to discharge points. This process is not possible in springs fed by distributed recharge that is transmitted through aquifer matrix porosity, such as unconfined aquifers in eogenetic carbonate rocks. Diffusely recharged water has a long residence time within the aquifer, and thus would have equilibrated with the aquifer rocks prior to discharge to the conduits. The upper Floridan aquifer has high matrix permeability (∼10−13 m2), and many springs lack discrete inputs of undersaturated allogenic water in their recharge areas. Consequently, another explanation for their development is necessary. During flooding of the Suwannee River in north-central Florida, water highly undersaturated with respect to carbonate minerals commonly recharges the upper Floridan aquifer through spring vents, and solution scallops oriented away from the vents suggest most dissolution along conduit walls occurs during these flow reversals. During a single flow reversal at the Peacock Spring cave system, flood water was capable of dissolving up to 3.4 mm of the conduit wall rock. Dissolution occurs as flow reversals follow preexisting features that include joints and paleo–water-table caves. Lack of speleothems in conduits in the upper Floridan aquifer has been used as evidence that the caves formed in the phreatic zone; however, flooding would dissolve any speleothems that may have formed during previous subaerial exposure. Conduit enlargement during flow reversals suggests that dissolution can progress in the normal upstream directions, and this process may be an important driver of dissolution in any karst aquifer with outflows to surface water that are subject to flooding. Flow reversals would also introduce dissolved organic carbon and oxygen into the groundwater and provide important energy sources for cave ecosystems as well as altering redox chemistry of the aquifer water.