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In most urbanized and agricultural areas of central Europe, the shallow underground is constituted of Quaternary deposits which are often the most extensively used layers (water pumping, shallow geothermic, material excavation). All these deposits are often complexly intertwined, leading to high spatial variability and high complexity. Geophysical data can be a fast and reliable source of information about the underground. Still, the integration of these data can be time-consuming, it lacks realistic interpolation in a full 3D space, and the final uncertainty is often not represented. In this study, we propose a new methodology to combine boreholes and geophysical data with uncertainty in an automatic framework. A spatially varying translator function that predicts the clay fraction from resistivity is inverted using boreholes description as control points. It is combined with a 3D stochastic interpolation framework based on a Multiple Points Statistics algorithm and Gaussian Random Function. This novel workflow allows incorporating robustly the data and their uncertainty and requires less user intervention than the already existing workflows. The methodology is illustrated for ground-based towed transient electromagnetic data (tTEM) and borehole data from the upper Aare valley, Switzerland. In this location, a 3D realistic high spatial resolution model of clay fraction was obtained over the whole valley. The very dense data set allowed to demonstrate the quality of the predicted values and their corresponding uncertainties using cross-validation., (© 2022. The Author(s).)