Recharge, storage and flow characteristics of a karst aquifer were identified by correlating the results acquired from hydrogeological and speleological studies, stream/spring hydrographs, dye tracer tests, and hydrogeochemical analyses. Drinking water needs of the city of Kocaeli (Turkey) are partly supplied by karst springs (discharge 20–843 L/s) and the karst aquifer provides baseflow to streams that flow into Yuvacık Reservoir. A multi-variate dataset for characterization of the hydrological behavior of the karst aquifer was created. Stream hydrographs indicated that the aquifer comprises interconnected multipartite reservoirs, exhibiting groundwater residence times of 11–125 days. Recession coefficients of these reservoirs, obtained from master baseflow-recession curves, were 0.008–0.092 day−1. Dye tracer tests showed that groundwater velocities between recharge and discharge points were 483–1,328 m/day. Conduit flow characteristics were generally dominant in the upper reservoirs of the karst aquifer, characterized with high recession coefficients (0.017–0.092 day−1). Deeper reservoirs had a small baseflow recession coefficient (0.008 day−1). Autogenic point infiltration mechanisms were important in the recharge of many karst springs that discharged at high elevations (603–830 m amsl). However, autogenic diffusive infiltration regions (e.g. karst plateaus at high elevations) contributed to the recharge. Dye tracer tests and cave mapping revealed that depression points, allowing fast recharge, require special attention for protection and sustainable management of the karst aquifer. The results obtained from multiple methods and their correlation help to characterize the complex hydrodynamics of karst systems, and they can guide local authorities when assigning protection zones to locally important karst aquifers.