Karst aquifer studies often focus on allogenic water inputs and large conduit flow. However, diffuse recharge can be significant, particularly in unconfined eogenetic karst aquifers that retain high matrix permeability. This study examines an unconfined region of the upper Floridan aquifer (USA) that hosts a sinking stream, its resurgence, and a large conduit system. Daily diffuse recharge was approximated using a water-budget method and ranged from 17% of precipitation during a low precipitation year to> 53% during the highest precipitation year, illustrating the highly variable nature of diffuse recharge in this region. The total allogenic input via the sinking stream over the 5years of the study was significantly larger than the volume of diffuse recharge. However, only about 2% of the allogenic recharge flows from the conduit into the surrounding aquifer. That flow is restricted to storm events when hydraulic heads in the conduits exceed those in the surrounding aquifer. The estimated volume of dissolution is similar for allogenic recharge and diffuse recharge to the unconfined region surrounding the conduits, but dissolution from the diffuse recharge is distributed over a larger area than dissolution from allogenic recharge. These results exemplify how recharge type impacts flow and water–rock interactions in eogenetic karst aquifers.