Previous studies involving environmental performance purely focus on analyzing environmental or waste treatment efficiencies. This study combines various aspects of environmental protection and establishes a non-radial network DEA approach to evaluate the performance of an environmental protection system. The empirical methodology assumes that the system consists of three stages: administrative, executive processes, and protection effectiveness. The executive process includes waste treatment and pollution auditing divisions. In addition to assessing efficiencies, the empirical evaluation further explores the internal and external influences on performances and contributes implications and suggestions for environmental policy makers. The proposed model is utilized to gauge the performance of an environmental protection system for 20 municipalities in Taiwan. The results indicate the following; (1) for improving environmental quality, the government needs to put forth greater efforts in environmental audits; (2) improving productivity per unit so as to increase achievements in the executive process is more important for raising performance on environmental work, in addition to increasing workers and equipment for environmental protection; (3) a high degree of industrialization negatively influences administrative efficiency and educated residents have a greater comprehension for administrative operations, which can help in efficient budget utilization. (C) 2014 Elsevier Ltd. All rights reserved.