The Brazilian Equatorial Margin (BEM) is an area of extreme importance for the paloceanography and paleoclimatology of the South Atlantic although still with a wide field for research. The scope of this work is improve the comprehension of this important region, with the paleoceanographic interpretation for the sedimentary evolution of the Ceará and Barreirinhas basins in the Cenozoic through a seismic stratigraphic approach. Multichannel seismic lines and bore hole geophysical data were analyzed to the construction of a depositional model for both basins. This model was created using seismic stratigraphy and horizon mapping techniques. As results, five chronostratigraphical markers were identified and two distinct phases defined: (1) Paleogene and (2) Neogene + Quaternary. During the Paleogene, the sedimentation became more controlled by marine influence, developing in a time of warm and humid climate and surface and bottom currents still incipient. During the Neogene and Quaternary, the North Brazil Current (NBC) and the Deep Western Boundary Current became more important in the sediment transport, erosion and rework in the BEM. During this period, it was also possible to identify the climatic changes effect on the sediment supply for both basins, and also the paleocirculation variations, especially with the weakening of the NBC and the Atlantic Meridional Overturning Circulation.