Submerged macrophytes play an important role in stabilizing the water environments, thus restoration of submerged macrophytes has been the key to the restoration of shallow eutrophic lakes. Meanwhile, mussel stocking has been conducted as a parallel measure for submerged macrophytes restoration, because the filter-feeding mussels can improve and maintain a higher water clarity which it will enhance the growth of macrophytes. However, mussels, acting as an important spawning substrate for bitterling, may also facilitate the population development of bitterling fish (the common name for cyprinid fishes from the subfamily Acheilognathinae). The effects of bitterling fish on aquatic ecosystems are not clear. In the present study, we conducted an outdoor mesocosm experiment to study the effects of bitterling fish on water quality, the growth of submerged macrophytes and the attached periphyton, and the relationship between mussel and macrophytes. Three treatments were set with 4 replicates for each group, they are control (without mussel and bitterlings), mussels (with Sinanodonta woodiana), and mussel-bitterlings treatment (with both A. woodiana and Acheilognathus macropterus), meanwhile all the mesocosms were planted with equal density and biomass of Vallisneria denseserrulata. The results showed that the presence of bitterlings significantly increased the concentrations of total phosphorus, total dissolved phosphorus, suspended solids (TSS, OSS and ISS) and Chl.a of phytoplankton, but not for total nitrogen and total dissolved nitrogen. At the end of the experiment, the growth rate (both RGR and total individual), root-shoot biomass ratio, and maximum leaf length of macrophytes did not differ significantly between the mussel and control mesocosms, while the mean individual biomass of macrophytes in the mussel group was significantly higher than that of the controls which may be related to the higher biomass of periphyton on the surface of macrophytes leaves, though not significant compared with the controls. However, the presence of bitterlings did not significantly affect the mussel-macrophytes relationships. In comparison with the mussel's treatment, although bitterlings did not affect the RGR and total individuals of macrophytes, the maximum length of leaves was higher in the mussel-bitterling mesocosms than mesocosms with mussels, while the root-shoot biomass ratio was lower. These changes may be caused by the much higher concentrations of nutrients, suspended solids, Chl.a of phytoplankton and biomass of periphyton on the surface of leaves induced by the bitterlings which may boosted the growth of macrophytes leaves. Our results have important implications for lake management and restoration: bitterling is a small omnivorous fish which is widely distributed in lakes in the middle and lower reaches of Yangtze River. Moreover, they are highly correlated with submerged macrophytes and recovered quickly after lake restoration, so the monitoring and management of the small omnivorous fish, like bitterling in our study, should be strengthened when restoring and managing of shallow lakes.