Zooplankton, as primary consumers, are essential for maintaining aquatic ecosystem health and function. Inland waterway transportation has garnered increasing attention due to its significant ecological impacts on aquatic ecosystems. This study examined shipping-induced water column disturbances on zooplankton communities along the Beijing-Hangzhou Grand Canal, comparing the shipping-affected mainstream with two undisturbed tributaries. Results demonstrated significant reductions in zooplankton density and biomass (P < 0.05), along with altered seasonal community composition patterns. The density and biomass of zooplankton, respectively, were 79.7% and 82.0% lower in the disturbed mainstream than in the tributaries. Mainstream diversity exhibited suppressed seasonal variation, evidenced by reduced seasonal variation coefficients in the Shannon-Wiener, Pielou evenness, and Margalef richness indices relative to tributaries. Additionally, ship disturbances changed the seasonal succession patterns of zooplankton, with the main dominant species shifting from a seasonal cycle of “Bosmina longispina-Bosminopsis deitersi-Nauplius-Brachionus angularis” in spring, summer, autumn, and winter to “Nauplius-Nauplius-Nauplius-Brachionus angularis.” These findings offer theoretical foundations for Beijing-Hangzhou Grand Canal conservation and restoration, while establishing an assessment framework for inland waterway shipping impacts.