This paper presents a simple method for representing upward capillary fluxes from shallow groundwater into the unsaturated soil column of the large-scale hydrological models generally used at low resolution in global climate models. The groundwater scheme implemented in the Total Runoff Integrating Pathways river-routing model in a previous study is coupled with the Interaction between Soil Biosphere Atmosphere (ISBA) land surface model. In this coupling, the simulated water table depth acts as the lower boundary condition for the soil moisture diffusive equation. An original parameterization accounting for the subgrid topography inside each grid cell is proposed in order to compute this fully coupled soil lower boundary condition. The impact of this coupling on the simulated water budget is evaluated over France for the 1989–2009 period. Simulations are performed at high (1/12°) and low (0.5°) resolutions. Upward capillary fluxes induce a decrease in the simulated recharge from ISBA to the aquifers and contributes to an enhancement of the soil moisture memory. The simulated water table depths are then lowered, which induces a slight decrease in the simulated mean annual river discharges. These differences do not affect the comparison with observations. As a consequence, the simulated river discharges and water table heads compare still well with observations for the two soil bottom condition (free drain or fully coupled). It confirms the suitability of the coupling parameterization using subgrid spatial variability of topography. Compared to a free drain experiment, upward capillary fluxes at the bottom of the soil increase the mean annual evapotranspiration simulated over the aquifer domain by 3.12% and 1.54% at high and low resolutions, respectively. This increase can locally reach 50% and 30%, respectively.