Thermal destruction of chemical munitions from World War I led to the formation of a heavily contaminated residue that contains an unexpected mineral association in which a microbial As transformation has been observed. A mesocosm study was conducted to assess the impact of water saturation episodes and input of bioavailable organic matter (OM) on pollutant behavior in relation to biogeochemical parameters. Over a period of about eight (8) months, the contaminated soil was subjected to cycles of dry and wet periods corresponding to water table level variations. After the first four (4) months, fragmented litter from the nearby forest was placed on top of the soil. The mesocosm solid phase was sampled by three rounds of coring: at the beginning of the experiment, after four (4) months (before the addition of OM), and at the end of the experiment. Scanning electron microscopy coupled to energy dispersive X-ray spectroscopy observations showed that an amorphous phase, which was the primary carrier of As, Zn, and Cu, was unstable under water-saturated conditions and released a portion of the contaminants in solution. Precipitation of a lead arsenate chloride mineral, mimetite, in soils within the water saturated level caused the immobilization of As and Pb. Mimetite is a durable trap because of its large stability domain; however, this precipitation was limited by a low Pb concentration inducing that high amounts of As remained in solution. The addition of forest litter modified the quantities and qualities of soil OM. Microbial As transformation was affected by the addition of OM, which increased the concentration of both As(III)-oxidizing and As(V)-reducing microorganisms. The addition of OM negatively impacted the As(III) oxidizing rate, however As(III) oxidation was still the dominant reaction in accordance with the formation of arsenate-bearing minerals.