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We analyzed the temporal and spatial variation in water quality in the Huaihe River Basin influenced by the high level of fluctuation in rainfall and river flow in this transitional climate zone. To do so, we examined the relationship between water quality as measured by NH3-N concentrations and the precipitation and river discharge at key hydrological stations within the basin. The results indicate that flow regulation by hydraulic facilities had a significant negative effect on aquatic environment, but that including the preservation of environmental flows in management objectives could mitigate the problem. The existing hydraulic facilities should become the key tool to attain the multiple objectives that balancing the water utilization with the protection of environment and ecosystem health.