Based on hydrological, hydrochemical and hydrobiological studies made during 2010–2016 and considering the previous data, we discuss seasonal and interannual changes in the content of total and inorganic phosphorus on the Russian territory of the Selenga river. The study period is characterized by low hydraulicity of the river (especially in 2015) and short-lasting summer floods in 2012 and 2013. Concentrations of inorganic phosphorus varied within 0–174 μg/L, and total phosphorus varied from 28 to346 μg/L. Their maximum values are largely due to phosphorous inputs with sewage from economic facilities. It is shown that inputs of pollutants from the Mongolian territory are responsible for the increased phosphorus content levels in the river (as far as the river mouth) on the Russian territory, with corresponding local increases in phosphorus concentrations content manifesting themselves under the influence of anthropogenic factors. The lowest concentrations of inorganic phosphorus are recorded in the spring-autumn period with low hydraulicity and the mass development of the phytoplankton. During floods, high concentrations of inorganic phosphorus are recorded with an increase in flow velocity as well as with input of suspended solids and pollutants from the catchment area accompanied by a dramatic decrease of algal growth. In conditions of a long-lasting low water level since 1996, the Selenga has shown a tendency for a decrease in average annual concentrations of inorganic phosphorus and for an increase in the content level of its organic compounds. It is shown that outputs of both inorganic and total phosphorus by the river are governed by changes in the water runoff. During the 2010–2016 low water level, the output of inorganic phosphorus with the waters of the Selenga river decreased by a factor of 1,9–4,5, whereas the total phosphorus concentration increased by a factor of 2,9. The structure of phosphorus output to the lake has changed, i.e. outputs of inorganic and organic phosphorus decreased and increased, respectively.Keywords: phytoplankton, water runoff, phosphorus outputs, low water level, anthropogenic factors.