Along with the usual spooky and spine-tingling sights we have come to expect in caves, another scary inhabitant is turning up — contaminants such as PCBs, pesticides, dioxins, gasoline, fertilizers, sewage, and caffeine.
These pollutants, which are leaching into caves from the surface and groundwater, can pose a threat to the delicate underground environments that are prized by many, and that provide benefits to people, plants, and animals on the surface. The presence of these contaminants underground also serves as a blunt reminder of how pervasive pollutants are.
Caves tend to form in readily-dissolved rock formations such as limestone, gypsum, marble, and dolostone. These are known as karst formations, which underlie about 25% of the US, and are prominent worldwide. Karst formations have long been known to be pipelines for surface pollutants, but the full extent of their porosity, and the implications, are still unfolding.
- Karst maps. 
Another vulnerable geologic type is lava; caves and tubes occur in states such as AK, AZ, CA, HI, ID, NM, OR, and WA.
One recent example of documented contamination in a karst-formation cave is Tumbling Creek Cave in southern Missouri. This cave, in a rural, nonindustrial area, has the highest biodiversity of any cave west of the Mississippi River, and is home to three endangered species, according to a paper by the Missouri Department of Conservation's William Elliott,  573-522-4115 x3194, and others.
- "Waterborne Contaminants in Tumbling Creek Cave, Missouri," (pp. 107-123 in Elliott, W.R. (ed.), Proceedings of the 18th National Cave and Karst Management Symposium, October 8-12, 2007, St. Louis, Missouri): See the list of papers by Elliott;  click on 2008elliotttcc.pdf.
Contaminants in the cave included pesticides, PCBs, and polyaromatic hydrocarbons, often at low concentrations, but possibly still high enough to be causing some harm. Suspected sources include sediment disturbed by local development, and agricultural land uses.
High concentrations of PCBs and moderately high concentrations of dioxins have been found in Beacon Cave in the Bluestone River watershed on the border between West Virginia and Virginia. One person familiar with the study is West Virginia Dept. of Environmental Protection geologist Nick Schaer,  304-926-0499. Another is Virginia Dept. of Environmental Quality chemist Craig Lott,  804-698-4240. The team is still trying to figure out where exactly the pollutants are coming from. The site has novel traits, such as vertical karst bands, that make it difficult to track water and pollutant movement. The study was posted online in September 2007 by the US Geological Survey:
- "Estimation of Freely-Dissolved Concentrations of Polychlorinated Biphenyls, 2,3,7,8-Substituted Congeners and Homologs of Polychlorinated dibenzo-p-dioxins and Dibenzofurans in Water for Development of Total Maximum Daily Loadings for the Bluestone River Watershed, Virginia and West Virginia." 
Many other caves and contaminants are mentioned in Elliott's chapter on caves in the 2000 book Ecosystems of the World, 30: Subterranean Ecosystems:
- "Conservation of the North American Cave and Karst Biota:" See the list of papers by Elliott;  click on 2000conservbiota.pdf.
Among the contaminants were fertilizers, fecal coliform bacteria, salmonella, shigella, pesticides (including DDT), nitric acid, petroleum products such as gasoline and diesel, solvents, and sediment. Documented contamination occurred in AK, AL, IN, KY, MO, NM, TN, TX, VA, and WV, the Yucatan Peninsula and other sites in Mexico, and Vancouver Island in Canada. Among the possible sources of contamination are urban development, sewage, underground pipelines, leaking underground storage tanks, termite treatments of foundations, oil and gas drilling, medical waste, logging, and feedlots, grazing, and other agricultural lands.
Highly porous lava formations in Hawaii have contributed to an influx of road runoff, sewage, and agricultural contaminants in caves such as Kaumana Cave, and lavatubes in the Puna District, both on the island of Hawaii, and Offal Cave near Hana on Maui, says the Bishop Museum's Frank Howarth,  808-848-4164. Another potential contaminant he is concerned about is residue from genetically modified plants, which are widespread in Hawaii.
Another information source for cave contamination in both karst and lava formations is the fledgling National Cave and Karst Research Institute.  Construction is about to begin on its headquarters in Carlsbad, NM, and its Web site is under development.
- Penelope Boston, Assoc. Director of NCKRI, and Director of the Cave and Karst Studies Program, New Mexico Institute of Mining and Technology, 575-835-5657 (office), 303-579 4775 (cell), email. 
Boston, Howarth, Elliott, and others say there has been limited funding for studies of this realm. But the evidence available so far suggests that contamination of caves and other underground areas may be widespread.