Maintaining and improving the productivity of Japan as a whole is a major challenge amidst changes in its social conditions and climate. One conceivable countermeasure is urban restructuring to reduce the economic and social risks of flood damage. This study aims to shed light on the relationship between future urban structures and flood risk, and to seek a new course of flood control measures by linking river management and urban management. The study assumes the presence of multiple rivers and the risk of both inland flooding and river flooding, and examines the policy for linking the two types of management in the city of Toyama, which promotes a compact city strategy. The study confirms that the river management component of reducing inundation depths in areas to be protected and the urban management component of location optimization can be more effective strategies than complete flood control with continuous embankments. Additionally, the study shows the feasibility of efficient flood control strategies that account for future population distribution changes, and the possibility of reducing damage by applying urban strategies.