We present results of the first research into the thermal regime of the water column of man-made Lake Atomic (Semipalatinsk test site) performed in 2013–2015. The temperature data have shown a two-layer stratification of the water column. In the upper layer (0–30 m) there are significant yearly temperature variations caused by seasonal climatic changes and wind–wave mixing. In the lower layer (30–80 m) there is a stable nonlinear temperature distribution. This lake can be classified as meromictic, whose upper layer consists of weakly mineralized “light” water and lower one, of highly mineralized “heavy” water. This stratification prevents seasonal mixing of waters of the entire column (from surface to bottom).