<jats:p>Abstract. This article describes a modular ensemble-based data assimilation (DA) system which is developed for an integrated surface–subsurface hydrological model. The software environment for DA is the Parallel Data Assimilation Framework (PDAF), which provides various assimilation algorithms like the ensemble Kalman filters, non-linear filters, 3D-Var and combinations among them. The integrated surface–subsurface hydrological model is HydroGeoSphere (HGS), a physically based modelling software for the simulation of surface and variably saturated subsurface flow, as well as heat and mass transport. The coupling and capabilities of the modular DA system are described and demonstrated using an idealised model of a geologically heterogeneous alluvial river–aquifer system with drinking water production via riverbank filtration. To demonstrate its modularity and adaptability, both single and multivariate assimilations of hydraulic head and soil moisture observations are demonstrated in combination with individual and joint updating of multiple simulated states (i.e. hydraulic heads and water saturation) and model parameters (i.e. hydraulic conductivity). With the integrated model and this modular DA framework, we have essentially developed the hydrologically and DA-wise robust toolbox for developing the basic model for operational management of coupled surface water–groundwater resources. </jats:p>