The report concerns the problems of ecology in the Eastern part of the Gulf of Finland and the Neva Bay during the construction and operation of St. Petersburg Barrie Flood Protection (KZS). The Barrier of Flood Protection includes 11 stone-earth dams, 2 ship-pass and 6 water-pass, a bridge with a lifting span of 102 m long and an underwater road tunnel with a length of about 2 km. The developed KZS project provides free water exchange, which has a minimal impact on the hydraulic regime and ecology of the water area of the Neva Bay. The protective structures fully implemented a systematic approach to collect, divert and clean up the entire volume of polluted water from the marine section of the ring road around St. Petersburg. KZS does not have a negative impact on the sanitary regime of the Neva Bay, on the reproduction of fish stocks, including valuable fish species. Moreover, protective structures play a huge role in preserving biodiversity and rare species of near-water and waterfowl.