The understanding of streamflow generation processes is vitally important in the management of water resources. In the absence of the data required to achieve this, Integrated Surface-Subsurface Hydrological Models (ISSHM) can be used to assist with the development of this understanding. However, the standard outputs from these models only enable elicitation of information about hydrological drivers and hydrological responses that occur at the same time. This generally limits the applicability of ISSHMs for the purposes of obtaining an improved understanding of streamflow generation processes to catchment areas that do not exhibit significant storage, travel times or flow depletion mechanisms. In order to overcome this limitation, a previously published Hydraulic Mixing-Cell (HMC) method is improved so that it can be used to follow surface water derived from direct rainfall and groundwater discharge to the stream and adjacent overland flow areas. The developed approach was applied to virtual experiments (based on the Lehstenbach catchment in southeastern Germany), which are composed of two ISSHMs of contrasting scales: (1) a riparian wetland of area 210 m2 and (2) a catchment of area 4.2 km2. For the two models, analysis of modeling results for a large storm event showed complex spatiotemporal variability in streamflow generation and surface water-groundwater interaction. Further analysis with the HMC method elucidated in-stream and overland flow generation mechanisms. This study showed within a modeling framework that identification and quantification of in-stream and overland flow generation better informed understanding of catchment functioning through decomposition of streamflow hydrographs, and analysis of spatiotemporal variability of flow generation mechanisms.