Concentration of the mineral forms of nitrogen and phosphor in the limits of urban areas is for 30-40% higher than on adjacent territories used for agricultural activities. Organic forms of both elements predominate in soils and bottom sediments (about 80%). Nitrate form of mineral nitrogen predominates in the surface waters, while in the liquid phase of bottom sediment ammoniac nitrogen consists approximately 70% of mineral nitrogen. The concentration of mineral phosphor in liquid phase of bottom sediments is in 10-20 times higher than in surface waters. Superficial runoff is an essential source of pollution with nutrients of water ecosystems and in its accumulation in different functional zones of urban areas. The ration between ammonia and nitrate nitrogen in this component is around 1:1, while for mineral forms of nitrogen and phosphorus this is circa 10-12:1. Atmospheric precipitations are responsible for around 1-2% of all nutrient loads on environment in the municipality and ration between mineral nitrogen in superficial runoff and precipitations in average is around 30:1. The content of nutrients in the bottom sediments of lake ecosystems is in 2-5 times higher in comparison with the Raut river sediments. Such values for nitrogen and phosphorus indicate on permanent and significant pollution of water ecosystems in the Balti town with nutrients and an action plan for its reduction is necessary for general improvement of the state of environment in the municipality.