Mycoremediation is a form of bioremediation in which fungi are used to decontaminate the area. The term mycoremediation refers specifically to the use of fungal mycelia in bioremediation.

One of the primary roles of fungi in the ecosystem is decomposition, which is performed by the mycelium. The mycelium secretes extracellular enzymes and acids that break down lignin and cellulose, the two main building blocks of plant fiber. These are organic compounds composed of long chains of carbon and hydrogen, structurally similar to many organic pollutants. The key to mycoremediation is determining the right fungal species to target a specific pollutant. Certain strains have been reported to successfully degrade the nerve gases VX and sarin.

Mycofiltration is a similar process, using fungal mycelia to filter toxic waste and microorganisms from water in soil.