The Clear Creek Management Area has historically been a mining district because the area is heavily mineralized. Between 1850 and 1970, the area produced mercury which was used domestically and exported worldwide for use in pharmaceuticals, munitions, technology and mining. During the 1900s ore mining expanded to include gems, chromite, magnesite and chrysotile. With the closure of the New Idria Quicksilver Mine in 1972, chrysotile become the principal mineral extracted from the area by three major mining operations. But that too came to an end. The Coalinga Asbestos Mine shut down in 1977. The Atlas Asbestos Mine closed in 1980. The KCAC Mine was the last operating chrysotile mine within the United States and it ceased operations in 1998.

Gems are still actively mined in the region. The most notable is the semi-precious gem Benitoite, which is California's official state gemstone. Discovered in 1907, this gem is still mined on a 40 acre parcel of private property located in the middle of Clear Creek, known as the Benitoite Gem Mine. Another rare gem is the demantoid garnet. This stone is green, unlike most garnets which are red. Demantoid garnets are only found in the Ural Mountains of Russia, Mexico, Namibia and Clear Creek.

Because both the State of California and the Federal Government have erroneously classified all forms of asbestos as a carcinogen, the BLM has declared about 30,000 of the Clear Creek Management Area to be a "hazardous asbestos area" because of the natural occurrence of chrysotile. The serpentine mineral chrysotile is used to produce a safe commercial asbestos. The EPA has ignored the growing body of scientific evidence suggesting that chrysotile is not dangerous and that exposure to chrysotile does not put people at undue risk of disease. (See What is Asbestos? and Holmes Safety Association Bulletin, November 1998 and Mineralogy of "Asbestos" for more information.) In fact, a recent study published in Inhalation Toxicology published (Volume 15, Number 14/Dec 2003) "Comparison of Calidria Chrysotile Asbestos to Pure Tremolite: Inhalation Biopersistence and Histopathology Following Short-Term Exposure" concluded that chrysotile "fiber is not associated with lung disease." Also read Asbestos and Mercury in Clear Creek.

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