Abstract: Aquatic community dynamics in semiarid regulated rivers (i.e., river systems significantly regulated by human activities) are sensitive to environmental changes; however, the precise mechanisms by which external drivers shape these dynamics remain poorly understood. Focusing on the middle and lower reaches of the Daheihe River (a first-order tributary of the Yellow River), this study utilizes 36 sets of synchronous “three-waters” (water resources, water environment, and water ecology) monitoring data collected across four cross-sections from 2023 to 2024. By integrating a metacommunity dynamics model (MDM), cumulative dispersal volume (C_DV), and the relative dispersal potential index (R_DPI), we elucidate the niche characteristics, dispersal patterns and underlying mechanisms of phytoplankton, zooplankton, and benthic macroinvertebrate communities. Several key findings emerged. First, the three communities exhibited relatively broad ecological niches (0.80—1.00) across most environmental gradients, with a high degree of overlap in resource utilization (mean competition coefficient of 0.93). Nevertheless, a certain degree of ecological niche differentiation persisted among the communities. Second, spatial dispersal along the river axis exhibited a pattern of net upstream output and net downstream input, with zooplankton showing the highest dispersal potential (R_DPI = 0.44). Third, biotic interactions contributed significantly more to community dynamics (51%) than water quality (27%) and hydrological factors (22%), while exhibiting pronounced spatial heterogeneity along the river axis. These findings provide a scientific basis for the ecohydrological management of semiarid rivers and the coordinated governance of water resources, water environment, and water ecology.