Anthropogenic eutrophication is the main ecological problem of the Baltic Sea. However, there are many rivers entering the sea without monitoring points. The paper presents methodology for evaluation of the total phosphorus and nitrogen outflow unit discharges from catchment areas of such rivers. As example, we consider Russian part of the Finnish Gulf catchment area. The first stage of the methodology consists in determination of partial catchment areas of rivers with water runoff and the biogenic elements concentrations monitoring points. We must determine the watersheds upstream the monitoring points. The next stage of the exploration is determination of the watersheds spatial landscape structure and the relief features. The stages are processed by GIS-technologies. The same processing must be applied to catchment areas of the rivers without monitoring points. Thus, it is necessary comparison of the watersheds parameters of both the above-mentioned types by means of cluster analysis. As the result, we must determine analogue watersheds of the rivers with the monitoring points for the catchment areas without the points. Of course, the watersheds must have similar landscape structures and relief parameters. At the exploration next stage, we calculate the unit discharges from the analogue watersheds on the base of the monitoring data. The final exploration stage consists in evaluation of the biogenic elements outflow from the watersheds of the rivers without the monitoring points. The research results can be used for planning of actions for marine ecosystems biodiversity keeping and the water resources maintenance for fishery and recreation.