Both climate change and anthropogenic activities contribute to the deterioration of terrestrial water resources and ecosystems worldwide. Central Asian endorheic basins are among the most affected regions through both climate and human impacts. Here, we used a digital elevation model, digitized bathymetry maps and Landsat images to estimate the areal water cover extent and volumetric storage changes in small terminal lakes in Burabay National Nature Park (BNNP), located in Northern Central Asia (CA), for the period of 1986 to 2016. Based on the analysis of long-term climatic data from meteorological stations, short-term hydrometeorological network observations, gridded climate datasets (CRU) and global atmospheric reanalysis (ERA Interim), we have evaluated the impacts of historical climatic conditions on the water balance of BNNP lake catchments. We also discuss the future based on regional climate model projections. We attribute the overall decline of BNNP lakes to long-term deficit of water balance with lake evaporation loss exceeding precipitation inputs. Direct anthropogenic water abstraction has a minor importance in water balance. However, the changes in watersheds caused by the expansion of human settlements and roads disrupting water drainage may play a more significant role in lake water storage decline. More precise water resources assessment at the local scale will be facilitated by further development of freely available higher spatial resolution remote sensing products. In addition, the results of this work can be used for the development of lake/reservoir evaporation models driven by remote sensing and atmospheric reanalysis data without the direct use of ground observations.