Reestablishment of submerged macrophytes is considered important when restoring shallow eutrophic lakes. To improve water clarity and consequently the growth conditions of macrophytes, removal of plankti-benthivorous fish has been used. In subtropical shallow lakes, however, rapid recruitment of small fish, especially benthivores during restoration, may hamper early reestablishment of submerged macrophytes. Crucian carp (Carassius carassius) and Vallisneria natans are common species dominated in subtropical shallow lakes. To investigate the effect of small benthivorous fish on the growth of Vallisneria natans, a 28-day outdoor controlled experiment was undertaken in 12 mesocosms with three densities of Carassius carassius − low (10 g m −2), high (40 g m −2) and no fish (all in four replicates). The results showed that the fish significantly increased chlorophyll-a concentrations and periphyton biomass in both fish treatments, most significantly at high density for Chl a. This concurs with an increase in nutrient concentrations , likely mediated by fish sediment disturbance and excretion, and a reduction of zooplankton biomass (less algal grazing). Increased concentrations of inorganic suspended solids with increasing fish density further enhanced turbidity, causing shading of the macrophytes. Accordingly, the relative growth rate, ramet number and root/leaf ratio of V. natans decreased significantly at low and high fish density compared with the controls, but the effects did not depend on fish density. However, mean leaf length rose with increasing fish density, likely to allow the plants to obtain more light. Overall, our results show that not only large-bodied carp, as demonstrated frequently, but also small-sized crucian carp posed a constraint on submerged macrophyte reestablishment, and we conclude that crucian carp may hamper restoration efforts in subtropical shallow lakes. Restoration by biomanipulation should therefore target also small-sized crucian carp.