Future scenario analysis that recognizes the plural values of biodiversity is effective to bend the curve of biodiversity decline. This study conducted a quantitative scenario analysis combining the Nature Futures Framework (NFF) and process-based landscape model LANDIS-II at the Bekambeushi River Watershed in northern Japan. The BaU was set by referring to the recent trend of forestry and agricultural management. Three desirable scenarios, NC (Nature-as-Culture), NN (Nature-for-Nature), and NS (Nature-for-Society), were designed based on questionnaire surveys to stakeholders and local administrative plans. Landscape changes for each case were simulated with the LANDIS-II from 2015 to 2100. The both common and scenario-specific biodiversity indicators were evaluated. The common indicators focused on fundamental landscape characteristics. The scenario-specific indicators were introduced by considering the value perspectives represented by each corner of the NFF. In the NN scenario, both forest and pasture areas were abandoned and rewilded. In the NS scenario, the forest management was continued to produce timbers by intensive selective logging, and the pastureland abandonment was slowly progressed and converted for solar PV installation. In the NC scenario, the forest and pastureland, which shape the identity of residents, were managed even in 2100. Through this scenario exercise, we identified and discussed the challenges to operationalize the NFF on the local landscape.