In recent decades, a series of policies and practices for environmental flows (e-flows) have been implemented in China, with the sustainable development goal of balancing the utilization and protection of water resources among social, economic, and ecological needs. The aims of this study were to determine the main challenges and issues in e-flows implementation at different scales by analyzing policies and practices for e-flows in China, and to propose some recommendations for bridging the gaps between the science and implementation of e-flows. The gaps between the science and implementation of e-flows were found after review of literature, policies, and practices, and it was found that ecological flow was a more widely used term by the government, rather than e-flows, in implementation. The plans and effects of e-flows implementation are discussed in this paper and challenges of e-flows implementation are recognized: (1) limited water resources and uneven spatial and temporal distribution, (2) a weak scientific basis for e-flows implementation, (3) poor operability of e-flows science, and (4) ineffective supervision and guarantee measures. The recommendations are (1) to strengthen the scientific foundation of e-flows, (2) to improve effectiveness in application of e-flows science, and (3) to propose operable and effective supervision and guarantee measures. This paper elaborates the current understanding of e-flows science and provides practical recommendations for implementing e-flows and for improving the effectiveness in e-flows implementation. To bridge the gaps between science and implementation of e-flows and improve the operability of policies in future practices, more scientific research on practices is recommended through adaptive management.