This study investigates the ecological effects of weirs on water quality and phytoplankton communities in the South Han River (SHR) over a two-year period. By focusing on three key weirs—Kangcheon Weir, Yeoju Weir, and Ipo Weir—the research examines how artificial structures influence river hydrodynamics, nutrient cycles, and algal growth patterns. Utilizing water quality measurements, phytoplankton analysis, and environmental factor assessments, the study identifies significant fluctuations in water quality parameters and phytoplankton abundance across the surveyed points. The analysis reveals a direct correlation between environmental conditions such as temperature, flow rates, and nutrient concentrations, particularly nitrogen and phosphorus, and the proliferation of harmful cyanobacteria, notably Microcystis. This research highlights the critical role of comprehensive management strategies that consider hydraulic residence time, nutrient balance, and temperature regulation to mitigate the impacts of weirs on river ecosystems and improve water quality in the SHR.