The increased frequency of extreme rain events due to climate change has garnered attention in Japan. In 2018, the country enacted the Act of Climate Change Adaptation to formulate plans at national and local levels. The government has suggested the use of nature-based solutions (NBSs) across the country to address the increased risk of natural disasters. This study employs scenario analysis to examine the effectiveness of NBSs for the mitigation of flood risk and their implications on the provision of ecosystem services (ESs). Shiga prefecture in Japan enacted its own ordinance in 2015. This ordinance considers existing land use and building regulations to mitigate flood risk. The quantitative analysis assumes nine scenarios up to the year 2050, combining the current policy of Shiga and our original assumption of advance policy options to evaluate the future flood risk and ES. The analysis revealed that land use management can partially mitigate the flood risk by banning new residences and relocating residential land from flood-prone areas to safer areas and converting residential land into forest and paddy fields. It also suggests that both flood risk mitigation and provision of ESs can be further improved if local governments introduce a residence growth management strategy.