In this study, we developed an approach to assess water scarcity by considering both water quantity and quality, while at the same time explicitly considering EFR.We applied this quantity–quality-EFR (QQE) approach for the Huangqihai River Basin in Inner Mongolia, China.We found that to keep the river ecosystem health at a “good” level (i.e., suitable for swimming, fishing, and aquaculture), 26% of the total blue water resources should be allocated to meet the EFR.