In the south basin of Lake Biwa, Shiga, Japan, overgrown aquatic weeds (submerged macrophytes) impede cruising boats and cause unpleasant odors and undesirable waste when washed ashore. To address this socio-ecological problem, Shiga Prefectural Government implemented a public program to remove overgrown weeds and compost them ashore to conserve the lake environment, while coastal inhabitants and occasional volunteers remove weeds from the beaches to maintain the quality of the living environment. However, these effects are limited because of disjointed social networks. We applied an adaptive and abductive approach to develop community capability to jointly address this problem by sharing academic knowledge with local actors and empowering them. The initial multifaceted reviews, including interviews and postal questionnaire surveys, revealed that the agro-economic value of composted weeds declined in historical and socio-psychological contexts and that most of the unengaged public relied on local governments to address environmental problems. These findings were synthesized and assessed with workshop participants, including local inhabitants, governmental agents, businesspeople, social entrepreneurs, and research experts, to unearth the best solution. The workshops resulted in the development of an e-point system, called Biwa Point, to promote and acknowledge voluntary environmental conservation activities, including beach cleaning. It may contribute to enhancing the socio-ecological capability of communities. Additionally, ethical issues, such as publication of inconvenient truths, undesired interpretation by the researchers, and social constraints in research methods, arose through our research practice.