Kucuk Menderes River forms a rich coastal wetland inside in the Selcuk plain. Three saline/brackish lakes, one swamp and Kucuk Menderes River are these wetlands’ components. Alkaline-slightly alkaline type lakes are recharged from precipitation and karstic springs that discharge from marble-schist and marble-alluvium contacts in the northern and southern parts of the study area. Water types of the wetland are Na–Cl and Na–Ca–Mg–HCO3–Cl in both rainy and dry seasons. Both seawater intrusion and evaporation, as being the sources of the ions, justify the presence of Na–Cl, Na–SO4 and Cl–SO4, in the wetland water. Environmental isotopes were used to identify the relationship between wetland and groundwater in the Selcuk plain. The δ18O and δD composition of wetland area samples have changed between −6.42 to −4.56‰, and −36.40 to −23.80‰, respectively. The lakes and rivers are plotted on the mixing line by slope of 5.2 and these data indicate that wetland is affected from seawater intrusion. The recharge area that was sampled in order to compare the wetland has Ca–HCO3 water type with a neutral-slightly alkaline pH values and the main hydrogeochemical process is weathering the different types of silicates. Iron, manganese and selenium are the dominant minor ions due to the high biological activities and organic matters in the lakes. There are two contamination risks for this wetland: (1) waste disposal site and (2) water treatment plant where the purified waters are released into the river. EC, Al, As, Cd, Cu, Fe and Zn values exceed those of aquatic life standards. In the near future these sites will pose a danger for wetland wild life and surrounding irrigation water suppliers.