In the 20th century, global pollution of the atmosphere with acid-forming gas (sulfur and nitrogen oxides) emitted during fuel oil and coal combustion and ore smelting created the problem of acid precipitation and consequent acidification of soil and waters. The European Russia (ER) is a region with substantial industrial emissions of sulphur. Western Siberia (WS) is a region where development of the oil industry. Associated gas flaring with oil extraction leads to the formation of acid deposition, mainly due to nitrogen oxides. In 2010-2012, pioneer survey small lakes were carried out lengthways transect “north –south” in European Russia (298 lakes) and Western Siberia (162 lakes), from tundra to steppe ecoregions. The investigation demonstrated that, the acid lakes of anthropogenic origin occur in the humid region. Natural humic substances increase the acidic properties of waters in case influence of strong anthropogenic acids. Water acidification led to direct and indirect effects on biogeochemical cycles and aquatic ecosystems.