There is a worldwide ecological problem of anthropogenic eutrophication. The problem is especially serious one for the ecosystems of lakes, water-storage basins, and closed seas, such as the Baltic Sea. The eastern part of the sea is the Neva Bay. The water area is totally located within the administrative border of St. Petersburg and is influenced by the megacity. There is monitoring of the total nitrogen and phosphorus inflow into the Neva Bay with water of the Neva River and its spill streams. Nevertheless, there are watercourses entering the bay without points of monitoring. We presented the methodology for evaluation of the total nitrogen and substances outflow from the catchment areas without the monitoring points into the Neva Bay and the eastern part of the Finnish Gulf, and the evaluation results at the previous conferences SGEM2023 and SGEM Vienna GREEN 2023 “GREEN Science for GREEN Life”. However, there is the problem: “What is the unaccounted income influence on the bay ecosystem life?” If the influence is negligible, the authorities have not to organize monitoring points on the unaccounted watercourses. Otherwise, the authorities have to organize the monitoring points. The paper presents methodology for the problem solution by means of the ecosystem functioning computer simulation and some results of the numerical experiments. The influence significance is evaluated by modification of the Nash–Sutcliffe criterion.