The karst aquifer systems in southern Kentucky can be dynamic and quick to change. Microorganisms that live in these unpredictable aquifers are constantly faced with environmental changes. Their survival depends upon adaptations to changes in water chemistry, taking advantage of positive stimuli and avoiding negative environmental conditions. The U.S. Geological Survey conducted a study in 2001 to determine the capability of bacteria to adapt in two distinct regions of water quality in a karst aquifer, an area of clean, oxygenated groundwater and an area where the groundwater was oxygen depleted and contaminated by jet fuel. Water samples containing bacteria were collected from one clean well and two jet fuel contaminated wells in a conduit-dominated karst aquifer. Bacterial concentrations, enumerated through direct count, ranged from 500,000 to 2.7 million bacteria per mL in the clean portion of the aquifer, and 200,000 to 3.2 million bacteria per mL in the contaminated portion of the aquifer over a twelve month period. Bacteria from the clean well ranged in size from 0.2 to 2.5 mm, whereas bacteria from one fuel-contaminated well were generally larger, ranging in size from 0.2 to 3.9 mm. Also, bacteria collected from the clean well had a higher density and, consequently, were more inclined to sink than bacteria collected from contaminated wells. Bacteria collected from the clean portion of the karst aquifer were predominantly (,95%) Gram-negative and more likely to have flagella present than bacteria collected from the contaminated wells, which included a substantial fraction (,30%) of Gram-positive varieties. The ability of the bacteria from the clean portion of the karst aquifer to biodegrade benzene and toluene was studied under aerobic and anaerobic conditions in laboratory microcosms. The rate of fuel biodegradation in laboratory studies was approximately 50 times faster under aerobic conditions as compared to anaerobic, sulfur-reducing conditions. The optimum pH for fuel biodegradation ranged from 6 to 7. These findings suggest that bacteria have adapted to water-saturated karst systems with a variety of active and passive transport mechanisms.