High latitudes of the northern hemisphere are most vulnerable to climate warming, but impose a great threat due to positive feedback mechanism, such as enhanced greenhouse-gas emissions as a consequence of permafrost degradation. In the Russian Far-East, however, predictions are biased due to large research gaps. Hence, further investigations on recent climate patterns are essential to achieve better estimates for future environmental change in boreal Russia. In this context, open surface waters, such as lakes, provide valuable information about precipitation sources and seasonal variability in remote areas of Siberia. Stable water isotopes are good climate proxies due to temperature dependent fractionation process. Therefore, water, ice and snow samples were taken at a lake (Bol’shoe Toko, BT) in a little explored region in Southern Yakutia in 2012 and 2013. Analyses of the isotopic and hydrochemical composition were carried out to obtain a profound knowledge of the present hydrological regime. Water isotope analyses at Lake Bol’shoe Toko show only little variations spatially as well as throughout the water column. The mean isotopic composition of δ18O = -18.2 ± 0.2 ‰ and δD = -137 ± 1 ‰ show no significant seasonal variations comparing a summer and winter profile. There is no indication for evaporation enrichment found at Lake Bol’shoe Toko. However, fractionation alters the isotopic composition of surface waters during ice-cover formation. In contrast, water of the side lake “Bania Lake” (East of Lake Bol’shoe Toko) is enriched in heavy isotopes, indicating evaporative enrichment during summer, whereas water in a lagoon (South-East of Lake Bol’shoe Toko) have a slightly lower isotopic composition. Waters from all three lakes are of Ca-Mg-HCO3-type and show unpolluted freshwater conditions with low conductivity. However, nitrate concentration in the lagoon are at a critical level for algae growth. All in all, Lake Bol’shoe Toko is an oligotrophic, well-mixed, open through-flow lake system with no pronounced seasonal variability. Changes in isotopic and hydrochemical composition of the lagoon and Bania Lake are directly link to the geological and geomorphological setting of Lake Bol’shoe Toko, as precipitation and substantially surface run-off control the hydrological regime.