Gravel-bed rivers are an important source of groundwater recharge in some regions of the world. Their interactions with groundwater are complex and highly variable in space and time, with considerable water storage in the riverbed sediments. In losing river sections, where most of the groundwater recharge occurs, the river can be separated from the regional groundwater system by an unsaturated zone (i.e., perched). The complexity of groundwater–surface water interactions in these environments calls for the use of 3D fully integrated hydrological models to represent them, but their computational intensity limits their practicality for parameter inference, uncertainty quantification and regional scale problems. On the other hand, the simple groundwater–surface water exchange functions currently implemented in regional scale groundwater models are not suited to represent complex gravel-bed river systems such as braided rivers. There is therefore a need for developing groundwater–surface water exchange functions tailored to gravel-bed rivers that can be used in regional scale models. To address this issue, we developed a model simplification framework that combines a 3D integrated surface and subsurface hydrological model, a 2D cross-sectional river-aquifer model and a 1D conductance-based analytical model. We aim at broadly simplifying the 3D model while ensuring the appropriate simulation of groundwater recharge. We demonstrate our modelling approach on the Selwyn River (New Zealand) using piezometric data and groundwater recharge estimates derived from field observations and satellite imagery. Our results indicates that groundwater recharge from this river can be simulated using a simple 1D analytical model, which can easily be implemented in regional groundwater models (e.g., MODFLOW models). However, to represent properly the time variability of groundwater recharge, it is essential to use the groundwater level in the shallow aquifer associated with the river as input to the regional groundwater model. Our approach is generally transferable to other gravel-bed rivers but requires some observations of river losses for proper calibration.