Intensive and extensive water consumption and its potential negative impacts are increasingly challenging regional development in the Beijing-Tianjin-Hebei region (BTH). It is necessary to enhance the metabolic efficiency of both physical and virtual water, and the latter is often neglected in research and practical fields. The material flow analysis method was employed in evaluating spatiotemporal variations of the Water Resources Metabolism Efficiency (WME) for exploring the inherent driving mechanisms in the BTH region. Results indicate that the WME increased obviously and differently in Beijing, Tianjin and Hebei, as well as in the whole BTH region from 1990 to 2015. The changes in WME depend significantly on the improvement in society and economics. Water production and water consumption are crucial for the integrated metabolic efficiency of physical and virtual water, followed by other influencing factors, i.e., freshwater recycling use ratio (Rfw), total retail amount of commodities of unit water use (Cw), and industrial output value per cubic metre of water resources (Uio). The results could provide alternative references for efficient and effective utilization of water resources within and beyond similar cities.