This study applied the Korean framework of wetland management effectiveness evaluation to national wetland protected areas and identified key insights into developing a national wetland management policy. The framework is based on the basic evaluation framework of the International Union for Conservation of Nature and reflects the characteristics of South Korea’s wetland management policy. The evaluation framework comprises a total of 29 items and 21 detailed items in the design, appropriateness, and delivery sectors. Based on a cluster analysis, which considered the management levels of 22 sites that conducted first-stage self-assessment, the sites were divided into Groups A, B, and C. The second and third stages of qualitative evaluation were conducted on the representative target sites of each group by external research teams. The average score for the overall management level was the highest for Group B, followed by Groups C and A. Significant differences were observed among the groups for five items in the design sector, seven items in the appropriateness sector, and two items in the delivery sector. The management levels in the pilot sites were 43.9% in Yongneup of Mt. Daeam, 37.4% in the Damyang riverine wetland, and 59.8% in the Upo wetland, compared to the ideal condition. Important suggestions were derived through the evaluation framework. First, management effectiveness evaluation should consider national environmental and management policy characteristics based on an international framework. Second, an integrated management system should be established. Third, stakeholders should participate in building governance. Lastly, the participation of an external expert is essential.