Hydropower is among the most widely-adopted renewable energy sources worldwide. Its development has, however, led to environmental impacts such as carbon emissions and water loss. To date, the water footprint (WF) and carbon footprint (CF) of hydropower stations have been assessed, but not simultaneously or at a large scale such as national scale. Previous WF and CF studies rarely assessed all life-cycle stages of a hydropower station, calling for a more holistic understanding of the environmental impacts of hydropower. We developed a complete WF and CF assessment method and applied it to a case study on 50 of China's most influential hydropower stations, representing over 80% of the country's total hydropower. The total annual WF of these hydropower stations was 5.50 × 1011 m3, equal to 18.9% of Yellow River's annual runoff. The total CF of these stations was 1.06 × 107 tCO2e, with extremely large variations found, ranging from 1850 to 1.56 × 106 tCO2e. This study provides the first environmental impact assessment to simultaneously include the WF and CF of multiple influential hydropower stations at a national scale. We were able to show spatial variations in their environmental impacts from different life-cycle stages of the hydropower station. Most of the WF was due to surface water loss from reservoirs, while most of the CF was derived from the operational and maintenance stage of these stations. This initial WF and CF assessment of hydropower at a national scale provides insights for water resource management and carbon reduction during hydropower development.