Among the water sector problems the author emphasizes a need to improve both institutional structure of water resources management and methods of water use management at the level of basin. The current need to organize a system of payment for adverse impact on water bodies and an importance of dedicated water budget (or off-budget) funds for accumulation and allocation of funds collected in form of payments for water use, between federal and basin levels, are underlined. A need was observed to combine administrative and economic methods in water use and protection management, with gradual reduction in the part of administrative management methods.