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On the basis of water‐rock interactions, hydrogeochemical characteristics of spring, stream, wetland, and lake waters in the Mogan and Eymir Lakes special environmental protection area of Turkey were modeled using a reaction‐path simulation method. Geochemical characteristics of surface waters, mineralogical sources of ion concentrations in the springs, mixing, and evaporation/dilution relationships between the compositions of input flows and the lakes and between the compositions of inflows and wetlands were quantitatively determined. Major ion distributions in spring water reflect mineralogical characteristics of the lithologies that have been traversed by related springs before reaching the surface. Mixing and evaporation/dilution calculations show that approximately 41 to 83% of the ion concentrations in the Mogan Lake is provided by groundwater and the remaining is supplied by streams. In addition to the mixing, cation exchange and carbon dioxide (CO2) outgasing reactions are also required to obtain the observed lake composition. Chemistry of the wetland waters provided by Mogan Lake by way of groundwater and the regulator canal is primarily controlled by CO2 ingasing and exchange reactions. Small amounts of dilution by other sources are also required. The majority of ion concentrations in Eymir Lake water, on the other hand, is supplied by the wetland area. Ion concentration contributions of groundwater from other areas to the Eymir Lake are calculated to be approximately 8 to 59% of the total input. Silica precipitation, exchange, and evaporation are the effective processes in the production of Eymir Lake water concentrations. In general, the ranges of model results are consistent with those of hydrological data.