The Edwards-Trinity aquifer system is underlain by an extensive complex of rocks, ranging from Late Cambrian through Late Triassic in age, that are typically about 10 to perhaps 1,000 times less permeable than those composing the aquifer system. The Cretaceous rocks of the aquifer system are separated from the pre-Cretaceous rocks by an unconformity that spans about 60 million years of erosion during the Jurassic Period. The upper surface of the pre-Cretaceous rock complex forms the base of the Edwards-Trinity aquifer system. The configuration of the base reflects the original topography of the eroded pre-Cretaceous land surface plus the effects of subsequent deformation.

The most permeable pre-Cretaceous rocks are in the eastern half of the study area where they compose the Hickory aquifer (in Upper Cambrian rocks), Ellenburger-San Saba aquifer (Upper Cambrian- Lower Ordovician), and Marble Falls aquifer (Lower Pennsylvanian). These aquifers are hydraulically connected to the northeastern fringe of the Edwards-Trinity aquifer system, as their up-turned margins crop out around the flanks of the breached Llano uplift. The Rustler aquifer in rocks of Late Permian age underlies parts of the Trans-Pecos region, where it yields small amounts of greatly mineralized water for industrial and agricultural purposes. The Dockum aquifer in rocks of Late Triassic age directly underlies the Edwards-Trinity aquifer system in western parts of the study area, and locally increases the saturated thickness of the ground-water-flow system by an average of about 200 feet. Despite these notable exceptions, the collective effect of the pre-Cretaceous rocks is that 01 a barrier to ground-water flow, which limits the exchange of water across the base of the Edwards-Trinity aquifer system.