This paper examines the importance of examining the relationship between biology and geochemistry when designing a biopile to treat alkaline soils impacted by petroleum hydrocarbons. At a site in Nevada a large, unlined pit was constructed in a loamy sand soil and filled at regular intervals with a mixture of jet fuel, lubricating oils and waste solvents which were set on fire by the local fire department for training purposes. During its period of operation numerous chemicals were also dumped into the pit for disposal purposes, including dichlorobenzene and various chloroethylenes. As a result of these activities a large groundwater contaminant plume was formed. As a part of the site remediation process a decision was made to perform a limited source removal and excavate the top three to four metres of contaminated soil from the burn pit and place it in an engineered biopile. The location of the training pit is in a heavily mineralised basin where the background sulphate level in groundwater exceeds 5000 ppm. Due to naturally occurring biodegradation of the petroleum hydrocarbons a large portion of the sulphate was converted to sulphide which deposited in the soils as marcasite in the anaerobic soils. The initial attempt at soil remediation was to use a forced air treatment scheme that had worked well in small scale laboratory testing. Unfortunately, when attempted in the field on a large scale, marcasite reacted with atmospheric oxygen resulting in internal biopile temperatures exceeding 90C resulting in the virtual sterilisation of the soils without remediation occurring. In order to solve this vexing problem Pintail Systems, Inc developed an anaerobic culture that allowed the pile to be operated under anaerobic conditions. Within three months the biopile successfully demonstrated on a large scale significant biodegradation of the refractory petroleum hydrocarbons.