The Hutoubi Reservoir and its mainstream, Huyuan Stream, in the southern mountainous region of Taiwan, have experienced riverbed sedimentation and flood disasters for the past 150 years. In addition to climate change, it is necessary to scientifically consider its regulation for the next hundred years. This study adopted a collaborative approach, involving industry, government, and academia, using Nature-based Solutions (NbS) to enhance ecosystem services. The solution layout is constructed by widening the channel and constructing additional farm ponds and wetlands. An hydraulic simulation indicated that flood control was addressed. The restoration project would create diverse aquatic habitats by simulating and evaluating the distribution of ecological biotopes, using porous materials as revetments. It provided urban residents with forest leisure and recreational sites and supported the local agricultural and forestry products. The restoration has propagated local culture and created environmental and professional education. Therefore, ecological services are enhanced regarding regulation, support, provision, and culture. This pilot study, led by researchers, aimed to promote comprehensive management concepts considering all stakeholders and their active participation. We integrated NbS into the watershed and its river system as a pathway for facing the challenges of rapid urbanization and climate change and improving ecosystem services.