In present paper are submitted scientific-practical recommendations to combating active eutrophication phenomenon of ecosystems of Republic of Moldova, which, in the current period, because of irrational management of national water resources has reached catastrophic proportions. It focuses on friendly environmentally measures such as: the design of fisheries and their management by the principles of ecological aquaculture, biological improving of aquatic ecosystems with fito- planctonophagous and macro-phytophagous fish species, mechanical removal of macrophytes and excess accumulated silt, chemical water treatment with harmless environment reagents, etc.