Considering the problems of current water shortages and the weakness in the existing research, this study scientifically revealed the spatiotemporal varieties of water resources metabolism efficiency and driving factors in nine provinces (cities) in the Beijing-Tianjin-Hebei region, central and western regions of China from 1990 to 2015 in the perspective of heterogeneous resource endowments. The main results show that the water resources metabolism efficiency changed little from 1990 to 1995, and the overall trend has been obviously improved since 2000 from the time scale. From the perspective of spatial distribution, in the early stages, water resources metabolism efficiency was low with unobvious regional differences. Since 2005, more obvious regional differences occurred in the Beijing-Tianjin-Hebei region than in other regions. Waste virtual recycling use ratio, total retail sales of consumer goods of unit water use, forest coverage and fresh water recovery rate are the main driving factors of regional water resources metabolism efficiency.