Global warming is likely to have significant effect on the hydrological cycle. Some parts of the world may see significant reductions in precipitation or major alterations in the timing of wet and dry seasons. Climate change is one of the serious pressures facing water resources and their management over the next few years and decades. As part of the southern belt of Mediterranean Europe, Turkey is highly vulnerable to anticipated climate change impacts. The changes in global climate will seriously affect inland freshwater ecosystems and coastal lakes. Mogan and Eymir Lakes located in Central Turkey are shallow lakes that may be impacted significantly by climate change. The interaction between the lakes and groundwater system has been modelled in order to analyse the response of lake levels to climate change over a planning period of 96 years, beginning from October 2004 and ending in September 2100. The impacts of the emission scenarios of A2 and B1 of the Intergovernmental Panel on Climate Change (IPCC) on lake levels have been analyzed with the help of the lake-aquifer simulation model. The fluctuations in lake levels due to climate change scenarios are compared with the results of a scenario generated by the assumption of the continuation of the average recharge and discharge conditions observed for 1999 and 2004. The results show that very small, but long-term changes to precipitation and temperature have the potential to cause significant declines in lake levels and temporary drying of the lakes in the long-term. The impact of climate change on lake levels will depend on how these water resources are managed in the future.