The US EPA requires direct evidence of contaminant removal before bioremediation or natural attenuation can be used for site remediation. Microcosm studies are commonly used to provide this line of evidence; however, molecular biology tools may provide a better approach for biological forensic analysis of contaminated sites. DNA biomarker technology and laboratory scale microcosms were used to assess the feasibility of natural attenuation, biostimulation, and bioaugmentation for the remediation of a benzene and toluene (B/T) contaminated aquifer. Detection and subsequent increase of target aerobic catabolic and phylogenetic gene biomarkers corroborated aerobic B/T degradation observed in laboratory scale microcosms. Anaerobic biomarker and microcosm studies failed to produce evidence of anaerobic B/T biodegradation potential. Biostimulation (nitrate and sulfate addition) and bioaugmentation with a known anaerobic benzene degrading culture both failed to stimulate B/T removal. However, the addition of benzoate slightly stimulated the removal of benzene under anaerobic conditions. Collectively these results suggest this petroleum hydrocarbon aquifer is not strictly anaerobic and has the potential for natural attenuation processes under aerobic conditions. This research demonstrated the value of using DNA biomarkers as a tool for biological and abiotic forensic site investigations.