Variations in temperature and precipitation have direct impacts on the physical, chemical and biological characteristics of the shallow lakes. This paper examines the possible linkages between climate variables and the water levels of shallow interconnected Lakes Mogan and Eymir, located 20 km south of Ankara in Central Anatolia. The variations in the lakes' water levels during 1996-2015 are studied and the impacts of climate variables on the lake levels are assessed to address the long-term consequences. The nonparametric Mann-Kendall test was used to quantify trends in the climate variables and the lakes' level fluctuations between the observation periods 1998-2007 and 2008-2014. Statistical analyses results showed that precipitation and temperature have crucial influence on the variations in the lakes' levels. The projected increase in temperature and decrease in precipitation over the next century may produce substantial decreases in lake levels, with consequent drying of both lakes.