In 1996, Lake Baikal was declared a UNESCO World Heritage Site. It contains nearly 25% of the world’s fresh surface water. In recent years, anthropogenic impacts on the ecosystem of Lake Baikal have been increasing due to the development of industry in the region, expansion of the tourist infrastructure, and recreational areas of the coastal zone of the lake. In addition, an increase in the frequency of forest fires has already led to irreversible destructive processes in some areas of the lake. This project investigates the behavior of anthropogenic and natural atmospheric aerosols during forest fires that swept large areas of Siberia and their potential transportation onto Lake Baikal surface. It was found that quite substantial nano-size and submicron aerosol fluxes could reach the water surface and alter ecosystem of the lake. Such outcome is especially important as the amount of pollutants transported through the air–water interface during bush fire events is almost one order of magnitude higher as compared to the fire free scenario.