This chapter presents the author's original, multi-aspect concept of managing the eutrophication process, taking into account those aspects and problems, that were identified and analysed in the monograph and which must be taken into account when developing a strategy for managing this process at various levels. Starting from the basic assumptions of the functional direction of the system approach, the authors developed the holistic multilevel concept of eutrophication process managing, which takes into account the aspects currently ignored in routine practices of this process managing. The concept covers coordinated activities’ totality at various hierarchical levels of process management.