Main sources of pollution of the river Novaya, one of the most ecologically unfavorable water bodies in St. Petersburg, have been revealed on the basis of hydrological, hydrochemical and geochemical data. The river lost natural water supply and its length decreased by 4 times after the runoff from the upper part of catchment was redirected to the river Dudergofka during the construction of the Pulkovo Airport several decades ago. Currently, the river is a drainage system of agricultural territory, supplying a system of six connected ponds at urban area. The main ecological problem of the aquatic system under study has been found to be nutrient and organic pollution. Main reason of pollution is intensive agricultural activity at the catchment area. As a result, a huge amount of phosphorus, nitrogen and organic substances enters the hydrographic network. Low flow rate of the water system makes worse the development of negative processes in the ecosystem. The main polluter is a livestock enterprise located in the upper part of the catchment area. It discharges wastewater into the drainage system in the catchment area and manures agricultural fields directly adjacent to the riverbed. In accordance with the evaluation criteria of the degree of surface waters chemical pollution, approved by the Ministry of Natural Resources of the Russian Federation, the situation is assessed as extreme in the aquatic system, and at some sites - as a zone of ecological disaster by a number of parameters. No contamination of water and bottom sediments, as well as soils in the catchment area with priority organic pollutants previously entering from the airport territory was detected. Nutrient loading on the aquatic system of the catchment area from the agricultural enterprise has been calculated. It has been assessed that the use of the best available technologies for agricultural activity could reduce the phosphorus load by 9 % and the nitrogen load by 28 %. Currently, the calculated concentration of total phosphorus in the drainage system in the catchment area is 4 times higher than the hyper eutrophic state limit. An improvement in the ecological situation can be achieved by optimizing agricultural activity in the catchment area, periodical removal of some nutrients and organic substances by mowing macrophytes in the swampy floodplain area, establishing a coastal protective zone and increasing the flow rate as a result of the return of runoff from the upper part of the river catchment to the former course