Eight seismic reflection profiles, two dimensions, were collected in a sector of the Magdalena Shelf, Baja California, Mexico, which contains a forearc basin, providing a spatial view of faults and seismic reflectors in this basin. Two small asymmetric basins were configured; Tosco-Abreojos and San Lázaro controlled by the Tosco-Abreojos and Santa Margarita-San Lázaro Faults. These faults accommodate a great part of the transtensional stress in the shelf and control the bathymetry and show great deformation in the western sector. Seismic horizons illustrate that the depocenter of the San Lazaro basin reaches depths of ~4 km, while the Tosco-Abreojos account reaches depths of around ~5.5 km, being present at these depths a diffuse reflector that is considered the acoustic basement. Santa Margarita fault is present in the Santa Margarita and Magdalena islands, extending northwest, then stop presenting its relief represented by the San Lazaro fault, which is associated with the seismic activity resent reported for the region. Reflectors observed to the south of the region, previously reported by other works, were also observed in this area. However, there are new reflectors to the NW, which fill the spaces of both basins, taking a total of eight seismostratigraphic units. Unconformity is present throughout the region that separates the Neogene sequence from the Paleocene-Eocene sequence that fills the forearc basin. Below the unconformity, there is a huge packet of Miocene sediments. Structural height corresponding to the subduction complex that extends in the SE-NW direction along the Magdalena Shelf is present, which is considered as the acoustic basement and is attributed to the ophiolite rocks. This structural height can be related to the Alto Lagunitas, located in the central part of Baja California, where an ophiolite rock is also present. But Magdalena Shelf is more recent than the Alto Lagunitas since the said rocks in this place are younger arch. From the results obtained, Santa Margarita Fault should be considered for future risk studies, since it is tectonically active and its path passes near population centers, such as Puerto San Carlos.