Modeling groundwater flow and contaminant transport in industrialized and urbanized alluvial plains is challenging because of the dynamic nature of the strongly interacting river – groundwater system and the scarcity of data. An original combined regional – local scale approach is proposed and illustrated using data from a detailed hydrogeological characterization of a brownfield located next to a water-level controlled river in Belgium. An original combined regional-scale (zonation) and local-scale (pilot points) approach is proposed to develop and calibrate a groundwater flow model in this context, using the finite difference code MODFLOW-2000, with an automatic parameter estimation using PEST. Groundwater flows are calibrated in transient conditions using river water level fluctuations as the hydrologic forcing of the groundwater – surface water system, resulting in a detailed, spatially heterogeneous distribution of the hydraulic conductivity field. The model reproduces with great accuracy groundwater head variations and continuous Darcy flux changes at the aquifer-river interface as a consequence of river fluctuations. The resulting hydraulic conductivity pattern is validated afterwards using field observations on hydrogeochemistry and tracer test results. Based on the calibrated groundwater flow model and the spatial heterogeneity of hydraulic conductivity field, benzene transport simulations were performed using MT3DMS, considering benzene attenuation as quantified in-situ, along the groundwater flow path, using carbon isotopic fractionation. The model indicated that fluctuations in the river water were at the origin of back and forward movements of benzene plumes and it allowed explaining the absence of benzene close to the river-aquifer interface by ongoing sulfate-reducing processes and aquifer heterogeneity.