Water pollution caused by heavy metal leaves human beings exposed to various health risks. Although many studies have focused on the efficiency of industrial water use (IWU) systems, few studies further address analysis for the harmful effect of heavy metal polluted water on human health. This paper first considers both IWU and healthcare (HC) systems as an integrated two-stage IWUHC system. Detailed efficiencies and its dynamic evolution are further revealed by integrating a dynamic two-stage DEA model within a slacks-based measure and Kernel density estimation. Results are as follows: (1) During 2011–2017, the IWUHC systems for 30 provinces in China have low efficiencies, which may have been caused by the bad performance of HC sub-system. The rankings of the average IWU efficiencies in four regions are in agreement with that of HC sub-system: northeastern, eastern, western, and central regions. (2) Provincial differences of IWU efficiencies are more significant than that of HC sub-system. The two-level distribution of IWUHC efficiencies is not helpful for improving IWUHC efficiencies in the eastern and western regions. (3) Understanding the dynamic evolution of the detailed efficiencies and the key indicator efficiencies provide governments with differentiated and forward-looking suggestions toward promoting IWUHC efficiencies.