The article describes the results of studying the spatiotemporal variability of water quality in the Neva Bay located in the eastern part of the Gulf of Finland in the Baltic Sea. Assessment of water quality in the period 1988-2016 was performed using the pattern recognition model, which includes training and recognition systems. Recognition was done on 14 characteristics, combined into 4 private and 2 complex indicators. Causal relationships between water quality and its determining factors have been established. The quality of water is largely determined by the indicators of reservoir productivity and, to a lesser extent, the arrival of anthropogenic pollutants. The chemical composition of the Lake Ladoga water is used as the background for the Neva Bay on which discharges of nutrients from aeration stations are applied. The technology of deep wastewater treatment was introduced in 2005, which significantly improved the ecological situation in the Neva Bay. The main factor that inhibits eutrophication and worsens the quality of water is hydro technical works. The high turbidity of the water generated by limits the primary production and is the main factor preventing the flowering of water in the Neva Bay. From 1988 to 2003 the water quality was considered “clean”. Over the remaining years it has changed to become “moderately polluted”. In the space, the quality of water varies from “very clean” to the “contaminated” during the construction of the port “Marine Façade” of St. Petersburg.