The Upper San Pedro River Basin in Mexico and the United States is an important riparian corridor that is coming under increasing pressure from growing populations and the associated increase in groundwater withdrawal. Several studies have produced three-dimensional maps of the basin fill sediments in the US portion of the basin but little work has been done in the Mexican portion of the basin. Here, the results of a ground-based transient electromagnetic (TEM) survey in the Upper San Pedro Basin, Mexico are presented. These basin fill sediments are characterized by a 10–40 m deep unsaturated surficial zone which is composed primarily of sands and gravels. In the central portion of the basin this unsaturated zone is usually underlain by a shallow clay layer 20–50 m thick. Beneath this may be more clay, as is usually the case near the San Pedro River, or interbedded sand, silt, and clay to a depth of 200–250 m. As you move away from the river, the upper clay layer disappears and the amount of sand in the sediments increases. At 1–2 km away from the river, sands can occupy up to 50% of the upper 200–250 m of the sediment fill. Below this, clays are always present except where bedrock highs are observed. This lower clay layer begins at a depth of about 200 m in the central portion of the basin (250 m or more at distances greater than 1–2 km from the river) and extends to the bottom of most profiles to depths of 400 m. While the depth of the top of this lower clay layer is probably accurate, its thickness observed in the models may be overestimated due to the relatively low magnetic moment of the TEM system used in this study. The inversion routine used for interpretation is based on a one-dimensional geologic model. This is a layer based model that is isotropic in both the x and y directions. Several survey soundings did not meet this requirement which invalidates the inversion process and the resulting interpretation at these locations. The results from these locations were rejected.