© 2021 by the authors. Licensee MDPI, Basel, Switzerland.Fish, being an important consumer in aquatic ecosystems, plays a significant role by affecting the key processes of aquatic ecosystems. Omnivorous fish consume a variety of food both from pelagic and benthic habitats and may directly or indirectly affect the plankton community as well as the lake trophic state. We conducted a 72-day outdoor experiment in mesocosms with and without Prussian carp (Carassius auratus) to evaluate the effect of this often-stocked omnivorous fish on the plankton community and water quality. We found that the presence of fish increased the biomass of planktonic algae, total and inorganic suspended solids, leading to decreased light intensity in the water and a lower biomass of benthic algae. Fish also prevented development of submerged macrophytes and the establishment of large-bodied zooplankton. However, the fish did not increase nitrogen concentrations and even was lowered total phosphorus levels, in part due to nutrient storage in the fish. We conclude that stocking of Prussian carp should be avoided, or removed where stocked and abundant, to obtain good ecological quality of shallow lakes, characterized by clear water and high abundance of macrophytes.