In the present study, prey preference of juvenile fishes was examined using an experimental approach. Zooplankton composition, as a prey of the fish, was evaluated by taking into account the species as well as body size of juveniles in the aquarium. The predation of juvenile fishes is known to be an important factor in changes of zooplankton communities. In some previous studies at the regulated Nakdong River, the collapse of large cladcoerans and an increase in the rotifer population by selective predation during spring and summer were observed. This study focused on the predation of juvenile fishes such as Hyporhamphus sajori, Rhinogobius brunneus, and Opsariichtys uncirostris amurensis on zooplankton community structure in mesocosm scale experiments. These fishes selected the cladoceran Moina micrura with highest individual preference value (Manly/Chesson index)among zooplankton prey in the experimental aquarium. When the size-selective prey preferences of the juvenile fish were compared, both small (body size <2 cm) and large (body size >2cm) juveniles of O. uncirostris positively selected M. micrura. In the outdoor experimental tanks, juvenile fishes consumed the cladoceran M. micrura, resulting in an high abundance of the rotifer, Polyarthra spp. The results suggest that juvenile fish predation may play an important role in regulating the zooplankton community structure by reducing the cladoceran density and increase of rotifers in the Nakdong River during spring and summer.