This chapter presents problematic aspects of managing the eutrophication process, starting from the lack of a uniform definition of this process and discrepancies in the understanding of its essence, to various approaches to its research, mitigation and managing. Variety of widely adopted definitions of the eutrophication phenomenon were analysed and presented in the chapter. Different methodological approaches to understanding the eutrophication process were also presented: the metabolic approach and the balance approach. In this chapter the authors formulated their holistic approach and their own definition of eutrophication.