Microwave treatment of hazardous wastes like dioxin-contaminated soil potentially fills a great need for a remediation technology which potentially can be applied in-situ: the EPA has concluded from a risk assessment study that it is the excavation and transportation of such wastes that poses the greatest risk. Studies have been carried out on a surrogate for dioxin, namely, 9,10-anthraquinone because it has similar chemical and physical properties but it is not toxic. It was found in microwave treatment studies that, at temperatures attainable in-situ, anthraquinone became non-extractable. A model was proposed which postulated that as water was removed from soil aggregates, anthraquinone adsorbed directly on the humus and clay fractions, and then reacted chemically. This led to spectroscopic studies to determine directly whether or not anthraquinone did undergo a chemical reaction. Those studies were carried out using DRIFT (diffuse reflectance Fourier transform spectroscopy) and ATR/FTIR (horizontal attenuated total reflectance Fourier transform spectroscopy). Bands shifts and formation suggestive of possible chemical reactions were found after microwave treatment of anthraquinone adsorbed on humus and kaolin clay, respectively.