Abstract. Although integrated water resource models are indispensable tools for water management at various scales, it is of primary importance to ensure their proper fitting on hydrological variables, avoiding flaws related to equifinality. An innovative stepwise fitting methodology is therefore proposed, which can be applied for any river basin model, from catchment to continental scale as far as hydrological models or land surface models are concerned. The methodology focuses on hydrosystems considering both surface water and groundwater, as well as internal water fluxes such as river baseflow. It is based on the thorough analysis of hydrological signal transformation by various components of a coupled surface–subsurface hydrosystem in a nested approach that considers the conditionality of parameter fields on their input forcing fluxes. The methodology is based on the decomposition of hydrological signal in the frequency domain with the HYMIT (HYdrological MInimalist Transfer function) method (Schuite et al., 2019). Parameters derived from HYMIT are used to fit the coupled surface–subsurface hydrological model CaWaQS3.02 using a stepwise methodology, which relies on successive Markov chain Monte Carlo optimizations related to various objective functions representing the dependency of the hydrological parameter fields on forcing input fluxes. This new methodology enables significant progress to be made in terms of the spatial distribution of the model parameters and the water balance components at the regional scale. The use of many control stations such as discharge gauging stations with HYMIT leads to a coarse parameter distribution that is then refined by the fitting of CaWaQS parameters on its own mesh. The stepwise methodology is exemplified with the Seine River basin (∼76 000 km2). In particular, it made it possible to spatially identify fundamental hydrological values, such as rainfall partitioning into actual evapotranspiration, as well as runoff and aquifer recharge through its impluvium, in both the time and frequency domains. Such a fitted model facilitates the analysis of both the overall and detailed territorial functioning of the river basin, explicitly including the aquifer system. A reference piezometric map of the upmost free aquifer units and a water budget of the Seine basin are established, detailing all external and internal fluxes up to the exchanges between the eight simulated aquifer layers. The results showed that the overall contribution of the aquifer system to the river discharge of the river network in the Seine basin varies spatially within a wide range (5 %–96 %), with an overall contribution at the outlet of the basin of 67 %. The geological substratum greatly influences the contribution of groundwater to the river discharge.