There are considered results of the Neva Bay ecosystem functioning computer simulation. The water area is the Neva River estuary, which is the eastern part of the Baltic Sea. The main ecological problem of the sea ecosystem is its anthropogenic eutrophication. The Neva Bay has high recreation and fishery value. The Neva River is the very water-rich watercourse among the watercourses entering the sea with the most spacious catchment area. Saint Petersburg is situated at the mouth of the Neva River and on the Neva Bay coast. The city is the biggest megapolis among the Baltic Sea catchment area cities. Therefore, the Neva Bay ecosystem is influenced by the anthropogenic impact of the city and the Neva River watershed. We know amounts of the nitrogen and phosphorus income into the bay with the Neva River water inflow within the sewage and atmospheric precipitation. However, there is no information about the nitrogen and phosphorus outflow from the Neva Bay partial watersheds into the bay and its influence on the ecosystem trophic state. The paper is devoted to the problem decision.