There is a necessity for the Baltic Sea environmental protection against toxic contamination and anthropogenic eutrophication. The protection proposes an annual evaluation of the total nitrogen and phosphorus income into the Neva Bay from St. Petersburg. The evaluation takes into account the substances, which inflow into the Neva Bay with water of the Neva River and its spill streams. However, an additional source of the substances is the substances inflow by runoff from watercourses entering Neva Bay. The watercourses do not have monitoring points. There is an additional source of the elements, which is the nonpoint dispersed outflow of the substances from the Neva Bay shore. The paper presents the evaluation methodology of the nitrogen and phosphorus outflow of catchment areas without monitoring points and the
methodology verification result. The methodology uses data of analogous
watersheds with close spatial structure, drainage network density, and
average slope and so on. The methodology includes application of GIS technologies and cluster analysis. The paper presents some results of the
total nitrogen and phosphorus income into the Neva Bay with runoff of two
small watercourses.