Semi-permanent anthropogenic connectivity regulation in rivers, such as via weirs and dams, affects the plankton community. We hypothesised that the longitudinal similarity of the zooplankton community in a river could change in a river-reservoir hybrid system (RRHS). The impact of weir construction on zooplankton communities in terms of species diversity, abundance, and community structure was examined biweekly at six sites on the Nakdong River main channel for 14 years (before construction: 2002–2008; after construction: 2012–2018). We checked time series alignment using dynamic time warping between longitudinal survey sites, regardless of RRHS. Before and after RRHS, the zooplankton community showed an increasing number of species. RRHS decreased the longitudinal connectivity in terms of zooplankton species number and population density. Our study demonstrates that longitudinal zooplankton community trends can be used to study the connectivity of rivers and that longitudinal characteristics are disrupted in RRHSs.