Transient groundwater interactions and lake stage were simulated for Lake Barco, an acidic seepage lake in the mantled karst of north central Florida. Karst subsidence features affected groundwater flow patterns in the basin and groundwater fluxes to and from the lake. Subsidence features peripheral to the lake intercepted potential groundwater inflow and increased leakage from the shallow perimeter of the lake bed. Simulated groundwater fluxes were checked against net groundwater flow derived from a detailed lake hydrologic budget with short‐term lake evaporation computed by the energy budget method. Discrepancies between modeled and budget‐derived net groundwater flows indicated that the model underestimated groundwater inflow, possibly contributed to by transient water table mounding near the lake. Recharge from rainfall reduced lake leakage by 10 to 15 times more than it increased groundwater inflow. As a result of the karst setting, the contributing groundwater basin to the lake was 2.4 ha for simulated average rainfall conditions, compared to the topographically derived drainage basin area of 81 ha. Short groundwater inflow path lines and rapid travel times limit the contribution of acid‐neutralizing solutes from the basin, making Lake Barco susceptible to increased acidification by acid rain.