The aim of this research is to determine the relationship between groundwater flow and water quality of different ground and surface water basins in the southwest Turkey. In addition, groundwater vulnerability is assessed taking into consideration groundwater flow and quality. The autochthonous Beydaglari limestone is the major karstic aquifer in the region. According to the groundwater level map of alluvium aquifers in the basins, groundwater discharge toward the carbonate aquifer is direct and indirect. The hydrogeological connection between ground and surface water basins occurs via the karstic aquifer located at the bottom of the alluvium bottom. In Egirdir lake, water also discharges in the karstic aquifer via karstic sinkholes at the western border of the lake. In the research area, general groundwater discharge is toward the Mediterranean Sea by means of autochthonous carbonate system, according to hydrogeological investigations, research of lineament and hydraulic conductivities. This result is supported by the locations of lineaments and shore springs discharging from the limestone. In addition, spreading of contaminants via karstic aquifer to great distance has been clearly identified.