Güllük Coastal Wetland System (GCWS) that is located at the contact of Menderes Massif and Lycian Nappe consists of both brackish karstic (Güllük Lagoon-GLW) and saline (Boğaziçi Tuzla-BTW) ecosystems in western Turkey and protected as "National Wetland of Importance". This area is important for its unique wetland features, aquaculture, tourism, agriculture, Bodrum airport, and Güllük port facilities. The aim of this study is evaluating of GLW and BTW by hydrogeologically and hydrogeochemically for the first time together. Mixohaline GCWS is recharged from precipitation, streams, and brackish karstic springs. The Electrical Conductivity (EC) values of Limni Lake and Tuzla salt pan were measured as 15330 and 41000 μS/cm, respectively. EC values of brackish karstic springs are 17310 μS/cm approximately. From the coastal to the inland, the mixing ratio increases and reaches a maximum of 45% in Savranköy spring that discharge from the contact between Milas Formation and alluvium. The relationship between Na-Cl, SO4-HCO3 and Mg/Ca-Cl show that "weathering by ion exchange and/or seawater intrusion process". All the groundwater samples are NaCl water types. In parallel with these results, Gibbs, Schoeller and Piper Diagrams support the same seawater intrusion phenomena. Brackish karst springs first rose and then fell below sea level with epirogenic movements during the geological time and therefore karstification's progress. Samples are oversaturated with calcite, dolomite, and quartz minerals whereas, undersaturated with gypsum and halite minerals. Al, Cu and Zn values of some of the water samples exceed the tolerance limit of aquatic life standards. When the samples are evaluated in terms of irrigation water, brackish springs, and streams at Avşar and located near aquaculture farm, Lake Limni and saltpan have harmful effect to the plants due to their high Na concentration. These results suggest that the wetland is vulnerable because it is both in a sensitive karstic and a lagoon area category. Hydrogeological protected zones should be determined to ensure the sustainability of groundwater resources and to provide the country's economy.