Water resources in many respects define social and economic stability and direction of development of the country. Wellbeing and safety of the state in many respects is defined by water management and ecological safety, level of water availability of the population with qualitative drinking water, water supply of sectorsof economy, reliability and efficiency of forecasting of emergency situations on water objects, their timely prevention and minimization of the caused damage. Thus, water resources management, rational organization of economic activity, providing careful attitude to water are one of the most actual problems of country in general. The main approaches to water resources management in the Russian Federation at the solution of water supply problems, protection of waters and protection against high waters are considered at this article. The main problems and shortcomings of management system of water-economic complex in our country are revealed, the major limiting factors interfering further development of the water-economic complex are allocated and also the main ways of improvement of water resources management system are considered.