In order to ensure the integral management of water and land resources during the implementation of environmental protection engineering measures, as well as to solve ecological problems, a macroeconomic approach directed at the final results is necessary. The traditional "narrow" economics of nature use is viewed as a single cycle of water and land resources and production waste and pollution, with insufficient attention paid to the economy itself ("black box"). For purposeful use of macroeconomics, it is necessary to build a vertical of natural productivity of each natural resource (chain), which will connect the primary natural factors with the production of final products. An effective concept of the rationalization of nature use and environmental protection against debris-flow phenomena and the matching economic mechanism of nature use in sectors and complexes can be developed and realized only after the development of the concept of development of the sector complexes and the whole economy. Regional features of the formation of the economic mechanism of nature use are important. The assessment of economic efficiency indicators of environmental protection measures during the construction of hydraulic engineering structures is discussed. The value of efficiency obtained by environmental activities is considered by the criteria for evaluating the efficiency of the investment project, where this criterion is called net discounted income, net discounted value, or modern net income. Functional-value analysis of environmental impact during the construction of hydraulic engineering structures, including the construction of high dams, for the realization of the analytical stage, a functional model is built based on the orography of the social-ecological-economic system. Based on theoretical and field scientific studies, the economic efficiency of the innovative debris-flow control structure has been established, the numerical value of which is equal to 16.15 USD per 1 longitudinal meter of the structure.