China has developed more than 20 water pollution control plans for river basins (RBWPs) since 1996. However, the implementation has generally lagged. This paper proposes a three-step, post-evaluation methodology to analyze the implementation result of a RBWP and its influential factors. First, a multi-attribute evaluation method based on an index system is established to score the enforcement results of a RBWP. Indicators measure how well a RBWP has achieved its objectives, which include water quality compliance, pollution load control, project construction, financial inputs, and related management requirements. Second, an interpretive structural model is used to detect the significant factors that affect RBWP implementation. This model can effectively analyze the cause-effect chain and hierarchical relationship among variables. Five groups of factors were identified, namely, plan preparation, water resource endowment, policy, institution, and management. Both qualitative and quantitative methods are employed in the third step to evaluate the extent to which these factors have influenced the execution result of a RBWP, including pre-post contrast, scenario analysis, and correlation analysis. This research then post-evaluated the implementation of the Huai River Basin water pollution control plans (H-RBWPs) over a period of 10 years as a case study. Results showed that the implementation of the H-RBWPs was unsatisfactory during 2001–2005, although it improved during 2006–2010. The poor execution of these plans was partially caused by the underestimation of regional economic development in combination with ineffective industrial structure adjustment policies. Therefore, this case study demonstrates the feasibility and flexibility of the proposed post-evaluation methodology.