The study identifies significant risks associated with improper water diversion strategies, including increased nutrient loading and heightened eutrophication risks during warmer seasons. Cyanobacterial blooms, dominated by Microcystis and filamentous cyanobacteria, pose threats to water quality and ecosystem health. High flow rates from certain pathways, such as R1, were linked to elevated nutrient concentrations and algal gene copy numbers, exacerbating bloom conditions. These findings underscore the need for carefully calibrated diversion schemes to balance hydrodynamic improvements with reduced ecological risks.