In classical biomanipulation, piscivores fish is introduced to a water body which fed on planktivorous fish and causes an increase in the numbers of zooplankton and zooplankton by feeding on phytoplankton roots to reduction in algal blooms. In contrast, during non-classical biomanipulation piscivores fish is removed from the water body and planktivorous fish is introduced which fed on all kinds of plankton and led to improving the water quality parameters by reducing nuisance algae. Here, we examine the management of water quality parameters through non-classical biomanipulation by identifying problems and extract recommendations. Preference is given to non-classical biomanipulation due to certain hindrances with traditional biomanipulation such as planktivorous fish removal, increase in numbers of macrophyte and decrease in phosphorous (external and internal), respectively. In fact, non-classical biomanipulation can also be used to control algal blooms in tropical, highly productive lakes, where reduction in nutrient concentration is almost impossible. In spite of overlapping prey and predator spaces in closed environments, such as in tanks and ponds, similar results of non-classical biomanipulation were also obtained in lake ecosystems as well. Non-classical biomanipulation changed the community composition of phytoplankton at the start of trial in both enclosed water bodies and lakes. In our review of 30 studies, 63% of studies demonstrated successful control of phytoplankton with non-classical biomanipulation. Microcystis blooms were controlled efficiently by two planktivorous fish, bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), in Lakes Qiandaohu and Donghu, respectively. Eutrophic waters that lack sufficient concentration of macrozooplankton can be effectively managed through planktivorous fishes, such as bighead and silver carp. Non-classical biomanipulation is confirmed as an effective tool for the control of those nuisance algal blooms that cannot be controlled efficiently by large bodied herbivorous zooplankton while ineffective with blooms of nanophytoplankton species.