Semi-arid river basins, characterized by pronounced hydrological seasonality and anthropogenic pressures, face escalating threats to aquatic ecosystems under climate change. This study investigated the Dahei River Basin, a critical Yellow River tributary in Inner Mongolia, to unravel the coupled impacts of climate, geology, hydrological pulses and water quality degradation on eukaryotic plankton communities. Using alpha/beta-diversity, dispersal-niche continuum index (DNCI), co-occurrence networks, and Partial Least Squares Path Modeling (PLS-PM) across dry-wet seasons and habitats, key findings emerged: (1) Urban wastewater inputs create multidimensional resource gradients that drive niche expansion in rivers, challenging the conventional paradigm of reservoir-dominated niche variation. (2) Hydrological pulses asymmetrically regulate trophic dynamics: wet-season runoff enhances phytoplankton dispersal, while zooplankton utilize dormant egg banks for resilience. This seasonality also alters network stability, with wet-season connectivity increases cascade risks and dry-season modularity enhances disturbance buffering. (3) The PLS-PM analysis further clarified that alternating wet-dry phases reconfigure ecological pathways. These findings advanced understanding of semi-arid aquatic ecosystems by decoupling phase-specific stressor pathways. Based on these findings, we established a "hydrological phase-responsive framework" (HPRF) that integrates empirical results with management needs for semi-arid watersheds, emphasizing that restoration must dynamically align with wet-dry transitions for ecological integrity in water-scarce regions. This work advances frameworks for balancing ecological integrity and urbanization in water-scarce regions.