Karst aquifer systems are frequently host to diverse biological habitats that are inherently unique to the Earth’s subsurface. These ecosystems are directly linked to the hydrogeology through water that moves though the aquifer, and are subject to changes in water quality that may affect the health of a species or group of species. In many cases, karst aquifer ecosystems can be indicators of emerging water quality concerns that have yet to directly affect anthropogenic uses of the groundwater resource.