It is widely recognized that multi-year drought can induce changes in catchment hydrological behaviors. However, at present, our understanding about multi-year, drought-induced changes in catchment hydrological behaviors and its driving factors at the process level is still very limited. This study proposed a new approach using a data assimilation technique with a process-based hydrological model to detect multi-year drought-induced changes in catchment hydrological behaviors and to identify driving factors for the changes in an unimpaired Australian catchment (Wee Jasper) which experienced prolonged drought from 1997 to 2009. Modelling experiments demonstrated that the multi-year drought caused a significant change in the catchment rainfall-runoff relationship, indicated by significant step changes in the estimated time-variant hydrological parameters SC (indicating catchment active water storage capacity) and C (reflecting catchment evapotranspiration dynamics), whose average values increased 23.4% and 10.2%, respectively, due to drought. The change in the rainfall-runoff relationship identified by the data assimilation method is consistent with that arrived at by a statistical examination. The proposed method provides insights about the drivers of the changes in the rainfall-runoff relationship at the processes level. Declining groundwater and deep soil moisture depleted by persistent evapotranspiration of deep-rooted woody vegetation during drought are the main driving factors for the catchment behaviors change in the Wee Jasper catchment. The new method proposed in this study was found to be an effective technique for detecting both the change of hydrological behaviors induced by prolonged drought and its driving factors at the process level.