China’s socioeconomic transitions have dramatically accelerated its economic growth in last three decades, but also companioned with continuous environmental degradation. This study will advance the knowledge of heavy metal water pollution in China from a spatial–temporal perspective. Specifically, this study addressed the following: (1) spatial patterns of heavy metal water pollution levels were analyzed using data of prefecture-level cities from 2004 to 2011; and (2) spatial statistical methods were used to examine the underlying socioeconomic and physical factors behind water pollution including socioeconomic transitions (industrialization, urbanization, globalization and economic development), and environmental characteristic (natural resources, hydrology and vegetation coverage). The results show that only Cr pollution levels increased over the years. The individual pollution levels of the other four heavy metals, As, Cd, Hg, and Pb, declined. High heavy metal water pollution levels are closely associated with both anthropogenic activities and physical environments, in particular abundant mineral resources and industrialization prosperity. On the other hand, economic development and urbanization play important roles in controlling water pollution problems. The analytical findings will provide valuable information for policy-makers to initiate and adjust protocols and strategies for protecting water sources and controlling water pollution; thus improving the quality of living environments.