Understanding groundwater storage variations as a result of effects from both the vadose zone and the river is of critical importance in the hydraulically connected surface‐subsurface system. In this study, we present a novel Bidirectional Exchange Scheme in Surface and Subsurface (BE3S) that represents bidirectional exchanges between the vadose zone, phreatic aquifer, and river. The approach enables explicit representations of each flow regime while conserving mass, and successfully yields solutions of the coupled system for multiple temporal resolutions. We test the scheme by comparing the BE3S‐derived outputs against other models and corresponding observational data. We apply the scheme to simulate hydrologic states in a reach of the Brazos River in Southeast Texas, such as soil moisture content, groundwater level, and river stage as well as net subsurface discharge fluxes. Good agreements between the simulated and observed data for all the components show the suitability of the proposed scheme in modeling the bidirectional flows and exchanges. We also assess how the bidirectional hydrologic exchanges are affected by adjacent flow domains. We find that vertical percolation is significantly affected by unsaturated soil thickness, resulting in the spatial variability of vertical percolation across sloping topography. Hilltop‐to‐valley convergent groundwater flow is also found to impede vertical percolation in river valleys due to shallow water table while facilitating percolation in the hilltops. The capability of the presented scheme that accounts for the topographically driven lateral groundwater flow and drainage dynamics provides the potential to enhance the representation of the surface‐subsurface system in Earth System Models (ESMs). Plain Language Summary The hydrologic systems that comprise the Earth's surface and subsurface are linked and influence each other. Understanding how the systems interact is, therefore, essential to predict the hydrologic state of each flow system. The hydrologic interactions can be evaluated by quantifying exchange fluxes between adjacent flow domains. The characteristics of different flow systems can be modeled by the governing equation corresponding to each system, Besides, it is still necessary to clarify how could the time‐varying state of surface and subsurface waters due to the hydrologic/climatic forcing affect the direction and amount of exchange flux. We propose a novel numerical scheme to simulate the simultaneous interactions among vadose zone‐phreatic aquifer‐river on a sloping topography. The scheme is tested with a river reach of the Brazos River in southeast Texas as a case study and proved to have the successful capability to simulate hydrologic states such as soil moisture content, groundwater level, and streamflow as well as exchange fluxes. Our approach explicitly considers the mutual effects between a topographically‐driven drainage system and lateral groundwater flow. Overall, the presented modeling framework can be a viable tool to understand the interactive flows among different hydrologic systems in a linked fashion. Key Points Development and verification of a novel numerical scheme to represent bidirectional exchanges between the vadose zone, aquifer, and river Topographically driven convergent groundwater flow and its effects on vertical percolation are explicitly represented on catchment scale Combinational effects of the vadose zone and the river on groundwater vary by distance from the river, connectivity, and topography