Localizing sources of contaminated groundwater discharging to streams may be a challenging task. A detailed geological model of the site is required for simulating the groundwater flow and the contaminant transport, in addition to chemical and hydrological investigations. In the town of Grindsted, Denmark, contaminated groundwater discharges to a stream. Several contaminated sites are present in the area, where chemical waste from a nearby chemical factory was deposited. In order to understand the hydrological flow and transport of contaminants controlled by a few mostly continuous clay and lignite layers in an otherwise sandy environment, a detailed 3D geological model is constructed. The model integrates all available data including DCIP and EMI surveys, lithological logs from new and existing wells, hydraulic head and pore water electric conductivity data. This study addresses the challenges met while constructing the 3D geological model in an area, where inorganic contaminants are highly affecting the geophysical data. The model ambiguities related to interpretation of clay layers versus contaminated sand layers in the DCIP resistivity sections as well as resistivity/chargeability-thickness equivalences are managed by integrated interpretation of a large amount of different geophysical, geological, hydraulic and chemical data.