The Magdalena Shelf is a shallow, low-relief surface located along the Baja California Pacific margin. As part of a forearc basin, the shelf was a convergent margin setting before the oblique divergent plate boundary formed in the Gulf of California at 12 Ma. It is thought that since 12-8 Ma, this basin has been a transtensional or strike-slip basin. To constrain the geometry, structural characteristics and some stratigraphic relationships, an active-source, seismic-reflection study was carried out in the central part of the shelf. As a result, the analyzed data show faults, basins and unconformities. Two out of four observed basins are clearly controlled by the Santa Margarita and San Lazaro faults that dip similar to 40A degrees NE; a third basin is controlled by the Tosco-Abreojos fault. These three basins are part of the deformation zone that is associated with the Tosco-Abreojos fault system. The Iray-Margarita basin, on the other hand, is a fourth basin located at the northeast sector of the study area. An additional feature observed is a stepover lying between the overlapping ends of the Santa Margarita and San Lazaro faults. Small faults oriented sub-parallel to the above major faults are present, mainly throughout the western sector of the study area. Some of those minor faults cut through the seafloor indicating recent tectonic activity. Santa Margarita, San Lazaro and Tosco-Abreojos are also the names given to half-grabens controlled by the active faults that have the same names. The first two basins are affected by many more small faults in comparison with what we see in the third basin. Tectonically, this means that those two basins are the more active in the area of study. In all four basins, the upper seismic sequence consists of sediments controlled by faults of Neogene age. We found that the Iray-Santa Margarita basin is the deepest of all four basins (beyond the resolution of the data, > 5 km), and lack of minor faults there indicates that the basin is not tectonically active. Two unconformities are present in the region, unconformity-1 of Miocene age and unconformity-2 of Paleocene-Eocene and Cretaceous ages. Unconformity-1 is present in the entire region, while Unconformity-2 is present mainly in the Iray-Magdalena and San Lazaro basins. In the Iray-Magdalena basin the sedimentary sequences show an uplift that took place in late Jurassic time along its western portion. We also see that moderate compressive deformation increases gradually from west to east. A chaotic-reflector oriented NW-SE is observed with an irregular shape in all regions. It shows very superficial in some places, sub-parallel to the major faults and in association with the subduction complex. Seismic activity reported for the region showed a strong correlation with the fault plane of the Santa Margarita fault, indicating that the Tosco-Abreojos deformation zone is similar to 90 km wide in the area. Finally, the Santa Margarita fault should be considered in future hazard-risk assessments because of their proximity to Puerto San Carlos. As it has been reported, local seismic events (M < 4) have generated alarm in the local populace, as well as soil liquefaction and minor damage to structures in the region.