There is considered precise specification of total nitrogen and phosphorus income in the Neva Bay and the northeastern part of the Finnish Gulf ecosystems. The bay is the estuary located within the administrative border of St. Petersburg, the biggest conurbation on the Baltic Sea shore. The Neva Bay and the Finnish Gulf have significant fishery and recreation value. Anthropogenic eutrophication is the main danger to the Baltic Sea ecosystem. However, the danger is widespread, extending beyond the Finnish Gulf. Therefore, the presented methodology can be widely used for the evaluation of the biogenic elements incomes from the catchment areas of watercourses without monitoring points. The paper presents the evaluation methodology. It includes research of watersheds with and without data of the nitrogen and phosphorus outflow from them. The research consists of ascertainment of the watershed boundaries, determination of the watershed spatial structures, calculation of the biogenic elements unit discharges, cluster analysis and calculation of the nitrogen and phosphorus outflow from the catchment areas without the nitrogen and phosphorus outflow monitoring. The cluster analysis is used for the assessment of similarities and differences between the watersheds of watercourses with and without monitoring points. The results show a significant role of the nitrogen and phosphorus income from the watersheds without monitoring points.