This study was the first attempt to identify the sources of total oxidized nitrogen (TON) and inorganic phosphorus (IP) in the water of the Selenga River—the main tributary of Lake Baikal. To identify TON and IP sources, the data on nutrient concentrations in water of Selenga River and its tributaries as well as the data on river runoff were collected and mapped. On the basis of the obtained data, the values of TON and IP exported from different parts of Selenga watershed were evaluated and mapped using geospatial techniques. In addition, critical source areas (CSAs) which accumulate soil pollutants from nonpoint pollution sources and release them into the surface water during storm events were identified in most polluted watershed areas. It was found that the values of TON exports in most parts of the Selenga watershed varied in the range 0–50 kg/km2/yr, whereas the values of IP exports varied in the range 0–5 kg/km2/yr. Obtained data on TON export were in agreement with those obtained earlier by foreign researchers using global models of nutrient export, whereas data on IP exports were two times higher than those previously modelled.