• Impacts of hydropower plants on ecosystems are investigated. • Carbon-water-energy-ecosystem nexus of hydropower plants are analyzed. • Optimization is proposed based on path analysis. • 25.76% of the environmental impacts can be reduced. Hydropower plants are generally recognized as a climate-friendly approach to meeting growing energy demand, whereas the greenhouse gases from reservoirs and their considerable impact on ecosystems have been criticized. The interaction among these impacts remains unclear, especially with respect to hydropower plants located in high elevations. This study contributes to the multi-objective optimization of hydropower plants based on the carbon-water-energy-ecosystem nexus. To demonstrate the optimization framework, 37 hydropower plants located on the tributary of Yangtze River were selected. The results showed that their environmental impacts decreased with an increasing number of cascades, whereas the insufficient number of available hours exacerbates the environmental impact unit output. Uncertainty analyses further demonstrated the robustness of these results. Scenario analyses showed that a 25.76% reduction in the total environmental impacts could be achieved at the cost of 17.29% hydropower loss. The proposed framework can be used to optimize hydropower plants facing similar challenges globally.