The Palaeoproterozoic Onega Basin in northwestern Russia is an important geological archive for global events during oxygenation of Earth at 2.5–2.0 Ga. In this study, we make use of recent drilling results from the Fennoscandian Arctic Russia – Drilling Early Earth Project and the Onega Parametric Hole in combination with available gravity and magnetic data to illuminate the structure of the basin and its internal build-up. These drilling campaigns have provided new information on petrophysical properties (density, magnetic susceptibility) and stratigraphic thickness of the main horizons in the basin. We use this information in combination with gravity and magnetic data to construct a 3D crustal model of the basin with emphasis on its near-surface structure. Our near-surface structure is in agreement with previous findings and most of the gravity and magnetic anomalies are associated with known geological bodies. Modelling also suggests a lateral lithological subdivision of the upper Archaean crust into three parts. The central crust has a higher magnetic susceptibility of 0.12 (SI) and lower density of 2.7 g/cm3, while the surrounding upper crust in the western and eastern edge regions has a lower magnetic susceptibility of 0.075–0.1 (SI), but a slightly higher density of 2.75–2.8 g/ cm3. One possible explanation for the differences is the presence of highly magnetised magmatic rocks in the centre of the Onega region caused by magmatic activity resulting in lava flows and comagmatic shallow intrusions during the early Palaeoproterozoic.