The efficiency of nature-based facilities is mostly evaluated in terms of their pollutant removal capabilities; however, apart from water purification functions, constructed wetlands also perform ecological, cultural, and environmental education functions. A multi-criteria performance index was developed in this study to evaluate the overall efficiency of constructed wetlands. A total of 54 constructed wetlands installed across South Korea were monitored to evaluate the pollutant removal performance of the facilities. A comparison between the conventional pollutant removal-based evaluation and the developed multi-criteria index was also performed to determine the key changes in the results of evaluation when different methods are employed. Among the different types of wetlands studied, hybrid systems were found to be the most effective in terms of pollutant removal due to their complex configurations and functions. Newly constructed treatment wetlands have unstable performance and thus, a stabilization period ranging from two to five years is required to assess the facility’s pollutant removal capabilities. As compared to the conventional pollutant removal-based efficiency evaluation, the comprehensive evaluation method provided a more strategic tool for identifying the facilities’ strengths and weaknesses. Generally, the multi-criteria performance index developed in this inquiry can be utilized as a general tool for evaluating the sustainability of similar nature-based facilities.