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Hydrological changes affect not only the physicochemical factors and habitat structure of river ecosystems, but also the structure of biological communities sensitive to environmental changes, such as zooplankton. In this study, we investigate the effects of weir opening on environmental variables and topographic structures at Sejong Weir in South Korea and monitor the resulting changes in the structure and distribution of the zooplankton community. Weir opening led to increased dissolved oxygen and decreased conductivity, turbidity, chlorophyll a, total phosphorus, and total nitrogen and increased the diversity of topographic structures (reduced pool area and increase riffle and grassland/bare land areas) in the section downstream of Sejong Weir. Prior to weir opening (2015–2016), the cladoceran community was dominated by <i>Chydrous spaeericus</i> and <i>Moina microcopa</i>. After opening (2018–2019), the abundance of other cladoceran communities such as <i>Bosmina</i> groups (<i>Bosmina longiseta</i>, <i>Bosmina fatalis</i>, and <i>Bosminopsis deitersi</i>), <i>Ceriodaphnia</i> sp., and <i>Daphnia obtusa</i> increased. In contrast, the copepod species (<i>Cyclops vicinus</i> and <i>Mesocyclops leukarti</i>) were abundant before weir opening. We conclude that artificial weir opening helped maintain the unique environmental characteristics of the river ecosystem in terms of river continuity and led to a different zooplankton community composition in the new river environment.