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Helicopter-borne electromagnetic (HEM) measurements were conducted in Bexar County, Texas, to map subsurface electrical resistivity distribution in order to better understand the geology and hydrology of the Cretaceous Edwards and Trinity (Glenn Rose Limestone) aquifers. These karstic aquifers are classified as sole-source aquifers and thus are critical to the water supply for the area, including the large metropolitan area of San Antonio. The Glen Rose is divided in an upper and lower zone. The upper zone is subdivided into five hydrostratigraphic intervals based on lithology and fossil content. The lower zone consists of more massive limestone deposits. The apparent resistivity map derived from the highest frequency HEM measurements correlate with the known outcropping hydrostratigraphic intervals. The HEM maps show that the intervals can be further divided into resistive (limestone) and relatively more conductive (mudstone) units. One particular area has been chosen for detailed study where the upper Glen Rose Limestone has been exposed in two drainages with a 30 m flat top hill (mesa) between them. Standard 1-D Marquardt-Levenberg inversions fail to resolve the extension beneath the mesa of resistive fossiliferous limestone exposed in the drainage. Laterally constrained inversion recovers a more realistic layered resistivity model.