Hydrological models have been widely used to assess changes in stream discharges by climate change; however, concern might arise on the accurateness of the model predictions under the changed conditions particularly during low flow periods. In this study, two spatially distributed hydrological models MIKE SHE and WetSpa, each representing a different model complexity in terms of process description, data needs, parameter space, degree of calibration, were compared in their estimation of the climate change impact on the flow regimes in a medium-sized catchment in Belgium. The fully integrated, physically based MIKE SHE model, comprising a three-dimensional groundwater flow and river model, was applied to better understand the groundwater flow and groundwater–river interactions under changed climate conditions. Both models were able to capture the flow dynamics very well with high efficiencies and simulated the flow extremes very accurately. The groundwater heads in MIKE SHE and their seasonal variation had a high model performance. The two models simulated similar changes to future flows because of climatic changes. Peak flows were expected to increase or decrease depending, taking the large uncertainty in future climate trends into account. The model structural uncertainties on these high flow predictions were rather limited. Low flows were expected to reduce because of drier conditions by future climate change, indicating elevated low flow risks for Belgium. However, the projected low flow changes differed significantly over the models and even exceeded the uncertainty by the expected climate trends. Smaller impact was predicted by considering the groundwater physics and river interaction in the MIKE SHE model. These changes to the surface water regimes were verified by the changes in groundwater heads. Future groundwater conditions also point towards drier conditions with a small decrease in heads for future summer and autumn periods. Projected variations in winter heads depend on the climate scenario.