Demand for hydropower is increasing, yet the water footprints (WFs) of reservoirs and hydropower, and their contributions to water scarcity, are poorly understood. Here, we calculate reservoir WFs (freshwater that evaporates from reservoirs) and hydropower WFs (the WF of hydroelectricity) in China based on data from 875 representative reservoirs (209 with power plants). In 2010, the reservoir WF totaled 27.9 × 109 m3 (Gm3), or 22% of China’s total water consumption. Ignoring the reservoir WF seriously underestimates human water appropriation. The reservoir WF associated with industrial, domestic and agricultural WFs caused water scarcity in 6 of the 10 major Chinese river basins from 2 to 12 months annually. The hydropower WF was 6.6 Gm3 yr−1 or 3.6 m3 of water to produce a GJ (109 J) of electricity. Hydropower is a water intensive energy carrier. As a response to global climate change, the Chinese government has promoted a further increase in hydropower energy by 70% by 2020 compared to 2012. This energy policy imposes pressure on available freshwater resources and increases water scarcity. The water-energy nexus requires strategic and coordinated implementations of hydropower development among geographical regions, as well as trade-off analysis between rising energy demand and water use sustainability.