Almost all of the water from agricultural dams located to the upper of the Yeongsan river is supplied as irrigation water for farmland and thus is not discharged to the main stream of the river. Also, most of the irrigation water does not return to the river after use, adding to the lack of flow in the main stream. As a result, the water quality and aquatic health of the river have become the poorest among the four major rivers in Korea. Therefore, in this study, several strategies for water quality improvement of the river were developed considering pollution reduction and flow rate increase, and their effect analysis was performed using a water quality model. The results of this study showed that the target water quality of the Yeongsan river could be achieved if flow increase strategies (FISs) are intensively pursued in parallel with pollution reduction. The reason is because the water quality of the river has been steadily improved through pollution reduction but this method is now nearing the limit. In addition, rainfall-related FISs such as dam construction and water distribution adjustment may be less effective or lost if a megadrought continues due to climate change and then rainfall does not occur for a long time. Therefore, in the future, if the application conditions for the FISs are similar, the seawater desalination facility, which is independent of rainfall, should be considered as the priority installation target among the FISs. The reason is that seawater desalination facilities can replace the water supply function of dams, which are difficult to newly build in Korea, and can be useful as a climate change adaptation facility by preventing water-related disasters in the event of a long-term megadrought.