We present an updated description of the San Felipe-Punta Estrella aquifer in Mexico by using new Transient Electromagnetic (TEM) measurements. A total of 17 TEM soundings were acquired with a 50 × 50 m2 single-loop configuration. The one-dimensional inversion of TEM data is performed by using Occam and Marquardt inversion techniques. A three-layer model, where a resistive layer is embedded by conductive ones, is sufficient to fit the data. The second and third layer are associated with the aquifer. We also applied Spatially Constrained Inversion (SCI) to the TEM data in order to derive a pseudo-3D model. A resistive layer extends from 10–100 m and is correlated to the permeable unit of the aquifer. The lowest conductive layer is associated to the semipermeable unit and starts appearing at a depth of 100 m. A high salinity in the permeable unit is detected at TEM stations near the shoreline, suggesting a saltwater intrusion. The TEM 1D inversion and SCI results confirm what a previous Vertical Electrical Sounding (VES) survey campaign has detected using electrode spacing up to 1,000 m. The bedrock of the aquifer structure could not be detected by the applied TEM configuration.