Small omnivorous fish often dominate in subtropical shallow lakes, and they may affect the community structure of aquatic organisms on at least two trophic levels. However, in the study of aquatic food webs in subtropical lakes, most ecologists have focused on the effects of large-sized omnivorous species (e.g. common carp), studies of small-sized species being scarce. We conducted a mesocosm experiment with two treatments (fish presence and absence) to examine the effects of a small-sized omnivore, bitterling (Acheilognathus macropterus), on phytoplankton, zooplankton and benthic macroinvertebrates. Our results showed that bitterling presence significantly increased the chlorophyll a concentration and biomass of phytoplankton, which became dominated by cyanobacteria (mainly Aphanizomenon spp.) that accounted for >99% of both total phytoplankton abundance and biomass. Both the abundance and biomass of zooplankton were also higher in the fish-present treatment, but small rotifers became dominant, and the zooplankton:phytoplankton biomass ratio decreased, indicating less grazing on phytoplankton. Moreover, both the abundance and biomass of benthic macroinvertebrates (tubificids) were higher in the bitterling-present treatment than in the controls, which is opposite to the situation found when omni-benthivorous fish (e.g. crucian carp) dominate. Higher biomass of tubificids may, in turn, result in higher sediment nutrient release. Our study suggests that A. macropterus, and maybe also other bitterling species, can alter both pelagic and benthic assemblages via both top-down and bottom-up control effects and lead to more turbid water in eutrophic lakes. Thus, more attention should be paid to these small omnivorous species in the restoration and management of shallow subtropical lakes.