Water management can improve the quality of valuable ecosystem services but can be costly to implement and the management costs are covered by national taxes collected by water users. Based on 30 valuation studies of water quality improvement from the Environmental Valuation Information System (EVIS) database provided by Korea Environment Institute (KEI), a meta-regression analysis was employed to measure the benefits that major river basins provided to the society. We compare these benefits to the costs, namely River Management Funds (RMFs) which are financial resources to support a variety of projects for managing and improving upstream water quality. Based on benefit-cost comparison, this study evaluates the efficiency of water resource management in South Korea. This study also provides policy options that are helpful to maintain the sustainability of water resource by improving the planning and performance of water management in the long run.