Large rivers are subject to flow regulation that profoundly alters the hydrological cycle. Such alterations and the resulting river degradation may be reversed by flow management measures such as long-term opening of weir gates. This study investigated the effects of opening the weir gates in the main channel of Yeongsan River, South Korea, which decreased the water level and water residence time, on the zooplankton community structure. Statistical analyses were performed on monitoring data of zooplankton and environmental factors before and after the gates were opened. The change in hydrological conditions substantially decreased the zooplankton abundance across major taxonomic groups (i.e., rotifers, cladocerans, and copepods). Consequently, after the opening of weir gates, the dominant species in the zooplankton community changed from aloricate rotifers to loricate rotifers. The zooplankton abundance tended to recover following the initial decrease after the weir gates were opened. In contrast to the abundance, the zooplankton richness showed less distinct changes in response to the weir gates being opened, which may indicate that most zooplankton populations can adapt to lotic environments. The results confirmed that hydrological factors are crucial to the zooplankton community structure in riverine ecosystems.