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• Present‐day thermal LAB depth of at least 250 km in southern West African craton. • Lateral changes in the lithospheric structure revealed by 3D resistivity modelling. • Cold and thick SCLM beneath the Baoulé-Mossi domain with relatively low water content. • Volta basin area likely defined by thinner and more enriched lithosphere. The West-African craton is defined by a combination of Archean and Palaeoproterozoic rocks that stabilised at ~2 Ga towards the end of the Paleoproterozoic Eburnean Orogeny, and therefore may reflect the transition from Archean to modern tectonic processes. Exploring its present lithospheric architecture aids further understanding of not only the craton's stability through its history but also its formation. We investigate the lithospheric structure of the craton through analysing and modelling magnetotelluric (MT) data from a 500-km-long east-west profile in northern Ghana and southern Burkina Faso crossing part of the Baoulé-Mossi Domain and reaching the Volta Basin in the south-eastern part of the craton. Although the MT stations are along a 2D profile, due to the complexity of the structures characterising the area, 3D resistivity modelling of the data is performed to obtain insights on the thermal signature and composition of the subcontinental lithosphere beneath the area. The thermal structure and water content estimates from different resistivity models highlight a strong dependence on the starting model in the 3D inversions, but still enable us to put constraints on the deep structure of the craton. The present‐day thermal lithosphere‐asthenosphere boundary (LAB) depth is estimated to be at least 250 km beneath the Baoulé-Mossi domain. The area likely transitions from a cold and thick lithosphere with relatively low water content into thinner, more fertile lithosphere below the Volta Basin. Although the inferred amount of water could be explained by Paleoproterozoic subduction processes involved in the formation of the Baoulé-Mossi domain, later enrichment of the lithosphere cannot be excluded [ABSTRACT FROM AUTHOR]