Results identified particular sensitivity in modelled recharge and stream flow to the different initializations, but reduced sensitivity in modelled energy fluxes. Analysis also suggests that to simulate a year that is wetter than the spin-up period, an initialization based on discharge equilibrium is adequate to capture the direction and magnitude of surface water–groundwater exchanges. For a drier or hydrologically similar year to the spin-up period, an initialization based on groundwater equilibrium is required. Variability of monthly subsurface storage changes and discharge bias at the scale of a hydrological event show that the initialization impacts do not diminish as the simulations progress, highlighting the importance of robust and accurate initialization in capturing surface water–groundwater dynamics.