Relevance. The efficiency of water management is determined by the quality of managerial decision-making. These decisions should ensure the balance of interests of all the actors in regional water markets. At present, in Russia, however, the balance of interests is considered only in macro-level strategies, which leads to the inefficiency of water distribution in regions. The study of the issues of rational distribution of water resources and their use in various industries and spheres of activity is, therefore, particularly relevant. Research objective. This article aims to propose methodology for maintaining the optimal balance between the interests of economic actors in regional water markets. Data and methods. This article proposes a program-modular approach to building a more efficient water management system. It is shown how the proposed methodology based on the incremental model of management can be used for balancing the interests of economic agents (suppliers and consumers of water resources). Results. It is proved that the plurality and divergence of interests of economic agents makes it difficult to manage them and thus precludes social and economic development of territories. The structural-functional analysis of the incremental model reveals various types of connections between the water-retaining capacity of gross regional product and indexes of industrial production for regions of the South Federal District. Conclusions. The prospects of development of water management in regions are associated with ensuring the balance of interests of the water market’s participants. The program-modular approach proposed by the authors combines the administrative and resource potential of regional water management and aligns the goals on the regional level with the more general goals of hydropower modernization. The novelty of our research is that it relies on the incremental model, which, unlike other models of management, leads to an incremental achievement of the desired through certain iterations.