Abstract This paper estimates water use efficiency of 31 provinces in China during 2004–2013 using slack based measure-data envelopment analysis (SBM-DEA) model which takes consideration of sewage. By using panel data model, factors that influence water use efficiency are explored. The results show that: (1) water use efficiency is higher in economically developed provinces such as Beijing, Shanghai and Tianjin. (2) In general, inefficiencies of labor input and water input are larger than that of capital input. (3) After taking into account sewage as unexpected output, inefficiency of gross domestic product (GDP) for each province is quite low, but most provinces have inefficient sewage emission. (4) It is found in the analysis of influencing factors that the ratio of added value of agricultural sector, water usage per capita and sewage per unit of output have negative impact on water resources use efficiency, while the import dependence and export dependence have positive impact. The results are robust.