A number of techniques, such as backstripping and forward modeling, have been previously used to reconstruct the tectonic, sedimentary, and thermal history at passive margins. Still, these techniques are generally inaccurate in places such as the west African margin where the stratigraphic record is disrupted by continuous faulting of the sediment pile caused by salt tectonics and by erosional unconformities. The ability to reconstruct the stratigraphy, salt thickness, and water depth along profiles of these types of margins is important for determining the factors controlling the geological history of the margin and the evolution of hydrocarbon systems. To reconstruct the stratigraphy, paleowater depths, and salt flowage on a profile across the Congo margin, we combined backstripping and palinspastic reconstruction. This enabled us to restore the faulting and salt flowage and simultaneously to take into account the isostatic response of the lithosphere to sediment loading and unloading. This method allowed us to estimate the paleowater depth, as well as the stratigraphy, and the geometry of the sedimentary section on the profile through time. The determination of the regional isostatic response of the lithosphere is performed with the use of a new model to estimate the flexural rigidity of continental lithosphere. To demonstrate this method, we perform the Cenozoic reconstruction of the Congo margin. The results yield a coherent geological history of the margin from the Eocene to the present. In the Eocene the margin was a carbonate ramp With a deep-seated shelf break (600 m). During the Eocene-Oligocene transition, intermediate water-depth oceanic currents triggered submarine erosion of the Eocene slope and shelf. From the Miocene to the present, we observe a large increase in the input of terrigenous elastic sediments. As a result, the shelf prograded 40 km across the Eocene ramp. As the elastic sediments prograded across the margin into the deep basin, faulting of the sediment pile and salt withdrawal caused the formation of grabens in places where salt swells had previously formed. Finally the reconstruction suggests that the Congo margin was uplifted by at least 330 m between the late Oligocene and the middle Miocene.