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Rapid expansion of juvenile fish after biomanipulation can delay the successful restoration of submerged macrophytes, leading to a turbid water status in subtropical shallow lakes. Aimed to test the effects of direct removal of juvenile crucian carp (Carassius carassius) on water quality and growth of two submerged macrophytes Vallisneria natans and Hydrilla verticillate, a short-term outdoor mesocosm experiment was conducted in the Taihu Laboratory for Lake Ecosystem Research (TLLER). The results indicated that the concentrations of TN, TP, suspended solids, and chlorophyll a decreased significantly with increasing removal density of juvenile crucian carp, thus resulting in a clear status of the water. Additionally, the mean relative growth rate of V. natans and H. verticillata in the low- and high-density removal treatments were higher than that in the controls. Moreover, the removal of juvenile crucian carp also significantly increased the stem length of V. natans, but no significant effect on that of H. verticillata. Meanwhile, the total number of V. natans and H. verticillata in the low- and high-density removal treatments was higher than that in the controls, but all of H. verticillata were lower than the initials. Our results indicated that removing juvenile crucian carp could improve the water quality, increasing relative growth rate, height, and reproduction of V. natans, and improving the survival rate of H. verticillata. The promotion of fish removal on the V. natans growth was greater than H. verticillata. The results also implied that it was necessary to continuously remove the juvenile benthivorous fish several times for restoring the submerged macrophytes in shallow lakes.