In the Khartoum region of central Sudan, Mesolithic sites were established on sandy ridges distributed along the Nile. Most of the excavations carried out in recent decades have revealed limited preserved archaeological structures or layers corresponding to subsequent phases of human presence due to the disturbance of the deposits. Post-depositional processes affecting Mesolithic sites include (1) the excavation of Neolithic to Post-Meroitic cemeteries at the same sites, (2) surface erosion, and (3) pedoturbation leading to the mixing of the stratigraphy. During a recent field operation along the western bank of the White Nile, archaeological contexts that were only partially disturbed were identified. Employing a geoarchaeological approach and the micromorphological study of sediments (supported by 14 C dating), settlements were placed in their paleoenvironmental contexts and differences between in situ Mesolithic layers and those disturbed by later processes were identified. Furthermore, it was possible to interpret the functional aspects of three categories of pits containing Mesolithic pottery (fireplace pits, fireplace pits with shell accumulations, and waste pits) and to discuss their significance within the wider framework of North African archaeology. Finally, this project has demonstrated the importance of integrating the geosciences (especially micromorphology) and archaeology in the study of processes leading to the formation and preservation of openair prehistoric sites in arid landscapes.