Abstract Rapid economic growth and urbanization in China have resulted in the dual threats of shortage of water and pollution of water. It is increasingly acknowledged that the efficiency of water resource system is influenced by not only the Water Use (WU) process, but also the process of Wastewater Treatment (WT). This paper considers both WU and WT as an integrated two-stage WUWT system to provide more comprehensive efficiency evaluation. In the first stage (WU subsystem), there are two parallel units, economic and social WU sub-minors, which consume water and capital to produce economic and social benefits. Meanwhile, the undesirable wastewater inevitably arises, which is treated in the second stage (WT subsystem). In order to assess the performance of the integrated WUWT system, an extended mixed network structure two-stage Slacks-Based Measure (SBM) Data Envelopment Analysis (DEA) model is developed to measure the detailed efficiencies and spot the weak link of the system. For case study, the provincial panel data during 2006–2015 of China are selected to verify the applicability of the proposed approach. Discussion is made from both time- and region-perspectives: over the ten years, the WU efficiencies are often higher than the WT efficiencies, so more actions should be carried out to improve the process of WT; from 2006 to 2011, social WU efficiencies are often lower than economic WU efficiencies, but the social WU efficiency has been improved after 2012; in terms of the overall efficiencies, the economically and socially developed provinces also have the higher efficiencies. Furthermore, the results demonstrate that the integrated WUWT system is efficient if and only if both WU and WT subsystem are both efficient, and the WU subsystem is efficient if and only if both economic and social WU sub-minors are efficient.