This article presents a scientific overview of the basic implementation of the principles of ecological engineering in watershed management. The first two sections discuss the landscape factors of nutrient fluxes and the critical source areas in rural watersheds. The subsequent sections give an overview of the principles, role and efficiency of the main ecotechnological measures used in watershed management: (1) riparian buffer zones and buffer strips, and (2) constructed wetlands for wastewater treatment. Examples of the design criteria, efficiency calculation and application efficiency of these two measures, as well as case studies on the application of ecotechnological measures in watershed management in various regions have been considered.