The environmental-economic focus of wastewater treatment and management attracts growing attentions in recent years. The static efficiencies and their dynamic changes are helpful to systematically assess the environmental performance of the water agencies and wastewater treatment plants (WWTPs). Additionally, identifying key factors of efficiencies is critical to improve the operation of WWTPs. In this study, the window method of data envelopment analysis (DEA) was applied to estimate the annual efficiency for four Canadian WWTPs and to explore the variations of annual efficiency under different window lengths. Meanwhile, the Tobit regression analysis was developed to determine the driving forces for WWTPs’ efficiency. The empirical results showed that: (i) the selected DEA window length remarkably affected both the average efficiency and the variations; however, it had no impact on the ranking of plants’ efficiency; (ii) lower efficiencies were observed in plants with larger capacities due to higher infrastructure and operation investments involved; (iii) both the influent total phosphorus concentrations and influent flow rates had significant effects on the WWTPs’ performance. Moreover, the staff and utility expenditures should be reduced to generate greater potential cost savings and efficiency improvement given the treatment technologies employed.