The water footprint in terms of the sum of both direct and indirect water cost of wastewater treatment is for the first time accounted in this work. On the basis of the hybrid method as a combination of process analysis and input-output analysis, a detailed water footprint accounting procedure is provided to cover the supply chain of a wastewater treatment plant. A set of indices intending to reveal the efficiency as well as renewability of wastewater treatment systems are devised as parallels of corresponding indicators in net energy analysis for energy supply systems. A case study is carried out for the Beijing Space City wastewater treatment plant as a landmark project. The high WROI (water return on investment) and low WIWP (water investment in water purified) indicate a high efficiency and renewability of the case system, illustrating the fundamental function of wastewater treatment for water reuse. The increasing of the wastewater and sludge treatment rates are revealed in an urgent need to reduce the water footprint of China and to improve the performance of wastewater treatment.