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All of the hydrogeologic subdivisions within the Edwards aquifer outcrop in Hays County have some porosity and permeability. The most porous and permeable appear to be hydrogeologic subdivision VI, the Kirschberg evaporite member of the Kainer Formation; hydrogeologic subdivision III, the leached and collapsed members, undivided; and hydrogeologic subdivision II, the cyclic and marine members, undivided, of the Person Formation.

The two types of porosity in the Edwards aquifer outcrop are fabric selective, which is related to depositional or diagenetic elements and typically exists in specific stratigraphic horizons; and not fabric selective, which can exist in any lithostratigraphic horizon. Permeability, the capacity of porous rock to transmit water, depends on the physical properties of the rock such as size, shape, and distribution of pores, and fissuring and dissolution.

Two faults, San Marcos Springs and Mustang Branch, completely, or almost completely, offset the Edwards aquifer by juxtaposing Edwards aquifer limestone against nearly impermeable upper confining units along parts of their traces across Hays County. These faults are thought to be barriers, or partial barriers, to groundwater flow where the beds are juxtaposed.

In Hays County, the Edwards aquifer probably is most vulnerable to surface contamination in the rapidly urbanizing areas on the Edwards aquifer outcrop. Contamination can result from spills or leakage of hazardous materials; or runoff on the intensely faulted and fractured, karstic limestone outcrops characteristic of the recharge zone.