While hydraulic groundwater theory has been understood as a viable approach for representing the role of the aquifer(s) in the surface-subsurface hydrologic cycle, the integrated modeling community still lacks a proper hydrologic structure to utilize the well-studied theory for large-scale hydrologic predictions. This study aims to present a novel hydrologic modeling framework that enables the Boussinesq equation-based depiction of hillslope-channel connectivity for applying hydraulic groundwater theory to large-scale model configurations. We integrated the BE3S’s [Hong et al., 2020] representation scheme of the catchment-scale Boussinesq aquifer into the National Water Model (NWM) and applied the NWM-BE3S model to three major basins in Texas (i.e., the Trinity, Brazos, and Colorado River basins). Since the NWM currently relies on a single reservoir model for baseflow estimation, theory-based evaluation was performed as the efficacies that the Boussinesq aquifer has relative to the single reservoir model should be consistent with hydraulic groundwater theory. We identified that the implemented Boussinesq aquifer(s) showed ‘more’ pronouced improvements in capturing streamflow dynamics than the original NWM as aquifers exhibited higher nonlinearities in the observed recessions. The varying degree of improvements in streamflow outputs according to the recession nonlinearities demonstrates (1) the applicability of the theory-based depiction of hillslope-channel connectivity and (2) the technical enhancement of model structure. We also examined the river states of all the reaches based on the represented bidirectional lateral hydraulic connections between the stream-aquifer and thus identified the dominant processes between the stream-aquifer (i.e., either river infiltration or baseflow) were spatially variable roughly following climatic gradients.