Stamets originally came up with the technique to control E. coli in the water outflow from his property. After planting a mushroom bed in the gulch where the water was leaving, within a year the coliform count had decreased to nearly undetectable levels. He discovered that the mushroom produced crystalline entities advancing in front of the growing mycelium, disintegrating when they encountered E. coli. As they did so, a chemical signal was sent back to the mycelium that, in turn, generated what appeared to be a customized macro-crystal which attracted the motile bacteria by the thousands, summarily stunning them. The advancing mycelium then consumed the E. coli, effectively eliminating them from the environment. 
One industrial application of mycofiltration has been to prevent erosion due to water runoff. Its primary application has been on abandoned logging roads. The approach here has been to place bark and wood chips onto logging roads, and inoculate this wood debris with mycelia of native fungal species. As the wood chips decompose, the mycelial networks develop and they act as filters to prevent silt-flow. In the process, they also renew topsoils, spurring the growth of native flora and fauna.
- source needed
- Lovy, Alenka; Knowles, Barbara; Labbe, Ronald; Nolan, Linda (1999), "Activity of Edible Mushrooms Against the Growth of Human T4 Leukemic Cancer Cells, HeLa Cervical Cancer Cells, and Plasmodium falciparum", Journal of Herbs, Spices & Medicinal Plants 6 (4): 49–58, doi:10.1300/J044v06n04_06
- The US Patent and Trademark Office Searchable website containing patents and applications related to mycofiltration