As the ecologically important recipient channels for riverine ecosystems, tributaries provide unique microhabitats for microorganisms, among which zooplankton constitutes the most important heterotrophic organisms. In particular, the reduced water velocity caused by dams is more favorable for zooplankton development; therefore, dammed rivers are expected to support extremely diverse and abundant zooplankton communities and notably different spatiotemporal distribution patterns. So far, however, only very few molecular studies support these assumptions. Using high-throughput sequencing, a high number of 350 operational taxonomic units (OTUs; 97% cutoff) were retrieved from 30 samples collected in the Xiangxi River, the nearest large tributary upstream of the Three Gorges Dam. Zooplankton did not show significant spatial distribution in the channel. Instead, the community structures varied significantly over sampling dates, corroborating the seasonal patterns found in lakes and ponds in the subtropical zone. As expected, the community compositions were deterministically governed by environmental filtering processes (phylogenetic clustering), in which water velocity appeared to be much less important than other investigated environmental factors. Moreover, most of the detected phylotypes (OTUs) had a relatively high (>90%) sequence similarity to previously deposited sequences, suggesting a mediocre degree of genetic novelty within the zooplankton communities in the Xiangxi River.