In restoration of shallow eutrophic lakes based on recovery of submerged macrophytes, stocking of the filter-feeding mussels has been commonly used for improving water clarity, thereby enhancing the growth of submerged macrophytes. However, the small omnivorous bitterling fish has to rely on mussels for breeding. Thus, the increased abundance of mussels may enhance the population development of bitterling. Nevertheless, the effects of bitterling (Acheilognathus macropterus) and their host mussels (Sinanodonta woodiana) on the aquatic ecosystems are, so far, not well-studied. We conducted a mesocosm experiment to study the effects of bitterling, mussels, and their interactions on water quality and the community structures of phytoplankton, zooplankton and benthic macroinvertebrates, respectively. Our results showed that bitterling did not substantially affect the concentration of inorganic suspended solids (ISS) indicating weak effects on sediment resuspension. However, the concentrations of total nitrogen and total phosphorus were significantly enhanced by bitterling. Consequently, both the abundance and biomass of phytoplankton were enhanced in the bitterling-only mesocosms, and cyanobacteria dominated the phytoplankton community at the end of the experiment. However, rotifers dominated the zooplankton community leading to a higher abundance of zooplankton in the bitterling-only treatment, while the total biomass of zooplankton did not differ significantly between the control and bitterling-only treatments. Moreover, bitterling significantly increased the total abundance of benthic macroinvertebrates compared with the controls, while the biomass of macroinvertebrates was not pronouncedly affected. The presence of mussels significantly eliminated the negative effects induced by bitterling, such as reducing the concentrations of nutrients, suspended solids and chlorophyll-a and phytoplankton biomass. However, the biomass of zooplankton and benthic macroinvertebrates were not substantially affected by the presence of mussels. Our results suggest that bitterling alone can induce significantly negative effects on water quality though mussels can eliminate part of these impacts under our experimental bitterling-to-mussel biomass ratio. Therefore, in the restoration and management of shallow lakes, more attention should be paid on the effects of small omnivorous fish, like bitterling, on aquatic ecosystems. The biomass of these small omnivores should be controlled at a relatively low level by physical (e.g., trap net) or biological (e.g., stocking of effective piscivorous fish) methods to minimize the negative effects of the fish on lake ecosystems.