This study uses the system approach as a method of describing the relations and interaction among natural and technogenic objects and the people to elaborate the basics of the methodology of creating and developing the Natural Environment-Object of Activity-Population (NENV-OA-PPL) class of natural engineering systems (NES) for managing water resources in various branches of economy. The methodological basics elaborated for the class of natural engineering systems in question have been translated into practice in designing, building, and running water-management facilities, referred to as objects of activity, in conformity with applicable regulatory environmental requirements in effect. The basic system notions defined for the considered class of systems according to the study results are structure, component, element, and the paramount role of the whole that includes the notions of natural and technogenic constituents and environmental acceptability. The study results were time-tested in the course of designing and building the Zelenchukskaya Hydroelectric-Pumped Storage Power Plant (HPSPP) located in the basin geosystem of the Upper Kuban in the Karachay-Cherkess Republic in the North Caucasus.