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This study aimed to determine whether a swimming-type (planktonic and epiphytic) zooplankton group compared with the taxonomic group is appropriate to indicate the environmental changes caused by dredging. Water sampling in the littoral zone was conducted from 2007 to 2015, including the dredging period from October 2010 to June 2012. The water quality, number of species, population densities, and biotic indices were compared for both dredging period and grouping type. Nine of 11 water quality parameters were changed by the dredging period. The results showed that the rotifer and planktonic groups were consistently dominant. In all groups, population density was the lowest during the dredging period. After dredging, both the number of species and population density increased only in the epiphytic group. The dominant species, including Polyarthra vulgaris, Brachionus calyciflorus, B. rubens, and Bosmina longirostris, were included in the planktonic group for 9 years. Evenness did not differ, but diversity increased after the dredging period. This study showed that zooplankton could be used as a supplemental biological assessment tool for evaluating the impact of river dredging.