This study analyzes the current state of the quality of surface waters in Russia. The main problems of quality management are identified. One out of every two residents of the Russian Federation is forced to use drinking water that does not meet the established standards for a number of indicators. The economic mechanism of natural water quality management is not aimed at solving the problem of its steady improvement, its outdated and controversial legislative and regulatory framework for governance, its low efficiency of supervisory activities, the imperfection of the monitoring and statistics system, or insufficient attention to the scientific and methodological base of quality management. Methods of regulation in Russia were formed more than 50 years ago. Modern approaches to monitoring the quality of surface waters, which have been intensively developed in developed countries in recent years, are not used. These include the analysis of xenobiotic content, the assessment of the influence of diffuse sources of water bodies’ pollution, and the use of modern mathematical models in regulating water quality. The necessity of the transition to a risk-based approach in the regulation of water quality is substantiated, proving the zero-risk concept currently in use does not achieve water quality targets.