We present here the methodology used to reconstruct six paleobathymetric and paleotopographic grids for six periods of age (~70, 66-60, ~45, 36-30, ~20, 12-5 Ma) based on the compilation of published onshore and offshore structural and sedimentary data. We provide xyz format (WGS84, z in metres) of the reconstructed geometry of the Mozambique Channel as well as the paleo-elevations of the East Africa and Madagascar landscapes. The compilation is beneficial both to the scientific community working in sedimentation, tectonics and for oceanographic modelling.