Omnivorous fishes are prevalent in warm waters and may have strong impacts on water quality by excreting nutrients and reducing periphyton biomass. However, most studies have focused on large-sized species and overlooked the role of small omnivores. Filter-feeding mussels may modulate the negative effects of small omnivorous fishes on water quality, and stocking of mussels has been frequently used in shallow eutrophic freshwaters in China to improve the water clarity. However, the mechanisms behind such management practices are poorly studied. We conducted a mesocosm experiment to examine the ecosystem effects of the bitterlingAcheilognathus macropterusas modulated by the musselSinanodonta woodiana, one of the mussels upon which it relies for breeding. We hypothesized that bitterling would exert negative effects on the lake environment, specifically higher phytoplankton biomass and lower water clarity, but that these effects might be alleviated by the filter-feeding activities ofS. woodiana. In a 56-d mesocosm experiment with and without bitterling in the presence and absence of mussels, we found interactive effects of bitterling and mussels. In mesocosms with bitterling, nutrient concentrations, phytoplankton biomass, and total suspended solids (TSS) increased, but there were no changes in periphyton biomass in the mussel-free treatments. In contrast to the effects of large-sized omnivorous fishes reported from the literature, bitterling mainly affected TSS levels by increasing organic suspended solids rather than inorganic solids, indicating weak effects on sediment resuspension. However, the presence of mussels alleviated the negative effects of bitterling by decreasing nutrient levels, phytoplankton biomass, and TSS concentrations. Mussels alone had no effects on periphyton biomass, but the mussel-bitterling interactions boosted the growth of periphyton. Our study suggests that the negative effects of bitterling on water quality (e.g., increased nutrient concentrations and phytoplankton biomass) are alleviated by the presence of filter-feeding mussels, but the stimulatory interactive effects of mussels and bitterling on periphyton may impair the recovery of submerged macrophytes.