Recovery of submerged macrophytes has been considered a key factor in the restoration of shallow eutrophic lakes. However, in some subtropical restored lakes, small omnivorous fish dominate the fish assemblages and feed in part on submerged macrophytes. Knowledge of the effects of small omnivores on the growth of submerged macrophytes is scarce and their responses are potentially species-specific, i.e. the growth of some species may be hampered by fish grazing while growth of others may be promoted by the nutrients becoming available by fish excretion. We conducted mesocosm experiments to examine the effects of the small omnivorous bitterling Acheilognathus macropterus, a common species in restored subtropical lakes in China, on nutrient concentrations and the growth of four species of submerged macrophytes (Hydrilla verticillata, Vallisneria denseserrulata, Ceratophyllum demersum and Myriophyllum spicatum). We found that the bitterling significantly increased nutrient concentrations via excretion and thereby enhanced the net growth of the less grazed nuisance macrophyte M. spicatum. In contrast, the net growth of C. demersum was reduced by the bitterling, most likely due to grazing as indicated by gut content analyses. Dominance by bitterling may, therefore, pose a threat to the long-term success of lake restoration by provoking a shift in the submerged macrophyte community towards nuisance species through selective grazing. Nutrient excretion may potentially also stimulate the growth of phytoplankton and periphyton, hampering the growth of submerged macrophyte.