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Introduction. The increasing shortage of water resources in the Republic of Crimea, due to water supplies from the external water source being shut off, emphasized the need to rationally use the existing water resource potential, which in turn requires a balance between the water users’ interests and maintaining a favorable environmental situation in the peninsula’s watercourses. Although in Russian and global practice there is a whole range of approaches to assessing the impact of natural and anthropogenic factors on the state of river geosystems, not all of them are applicable to solving the indicated problem. Methods. By testing integrated techniques, methods and models for assessing the impact of human activity on the stability of river natural and engineering systems (using the Zuya River as an example), we selected the most appropriate approach to develop viable solutions in water management. Results. By comparing the possibilities of using the scoring index method to assess the stability and vulnerability of watercourses to changes in physical and geographical as well as hydrological parameters and water quality, and methodology for the integrated assessment of the geoecological state of water resources of small rivers and the system model “Minor River Basin”, we revealed that only with the use of the latter it is possible not only to assess the real situation but also identify the reasons that impede the rational use of the peninsula’s watercourses. Conclusion. When developing decisions related to water management in the Republic of Crimea, the use of a suitable methodological approach to assessing the impact of natural and anthropogenic factors on the stability of river geosystems will make it possible to avoid mistakes when choosing measures and prioritizing actions aimed at the rational use of the existing water resource potential.