Previous studies on the characterization of hierarchically nested groundwater flow systems have mainly been based on the spatial distribution analyses of groundwater pathways. In this paper, by considering the discrete nature of the temporal behavior induced by different hierarchical flow systems, a new approach is proposed. The core of this approach is to use the critical residence times defined by the late-time peaks of residence time distributions (RTDs) to divide the groundwater flow field into local, intermediate and regional systems as described by Tóth (1963). We first introduce Tóthian basins of a 2D cross section and a 3D domain as synthetic test cases. The feasibility of the approach is demonstrated by comparing the partitioning results given by the dividing streamlines associated with internal stagnation points in the 2D Tóthian basin and by the hydraulic connections between recharge and discharge zones in the 3D Tóthian basin. Then, the Dosit River Watershed in Northwestern China is introduced as a field case study. Using the calibrated 3D groundwater flow model, one distinct late-time peak is identified from the RTD and indicates that the Dosit River Watershed can generally be regarded as a two-order nested flow structure with local and regional flow systems. This approach can be used to identify the volumes occupied by different orders of flow systems in 3D, and therefore opens up a new perspective in the study of the 3D nature of basin-scale groundwater flow.