The present study demonstrates and suggests a methodology for estimating watershed-scale storage changes from hourly discharge data in mountainous watersheds under a humid climate in Japan as the basis for watershed characterizations by combining a hydrograph separation and a storage-discharge formulizing method. Firstly, we separated hydrographs into different sub-components with respect to the time constants of the flow recession periods of the hydrograph by the filter-separation autoregressive method. Then we applied a storage-discharge formulizing method to the relationship between watershed-scale storage and discharge sub-components independently. As the result, we obtained a realistic estimate of annual watershed-scale storage change in the upper Abukuma River watershed. In addition, we compared our methodology with the non-linear reservoir modeling approach to explore the potential for extensive applications such as dominant process modeling, watershed classifications, and practical watershed management.