Both climate change and anthropogenic activities contribute to the deterioration of terrestrial water resources and ecosystems worldwide, with Central Asia and its endorheic lakes being among the most severely affected. We used a digital elevation model, bathymetry maps and Landsat images to estimate the areal water cover extent and volumetric storage changes for eleven small terminal lakes in Burabay National Nature Park (BNNP) in Northern Kazakhstan from 1986 to 2016. Based on the analysis of hydrometeorological observations, lake water balance, lake evaporation and Budyko equations, driven by gridded climate and global atmospheric reanalysis datasets, we evaluate the impact of historical climatic conditions on the water balance of the BNNP lake catchments. The total surface water area of the BNNP lakes decreased by around 7% for that period, mainly due to a reduction in the extent of three main lakes. In contrast, for some smaller lakes, the surface area increased. Overall, we attribute the decline of the BNNP lakes’ areal extent and volume to the prolonged periods of water balance deficit when lake evaporation exceeded precipitation. However, during the most recent years (2013–2016) precipitation increased and the BNNP lake levels stabilized.