The decay of organic matter of anthropogenic origin in a highly contaminated shallow groundwater system occurs permanently regardless of the availability of oxygen. Oxidation of organic matter smoothly changes from aerobic to anaerobic and vice versa. Hydrogeochemical transformations occurring in the interior of the contaminant plume are conditioned by the position in the 3D zone of the so-called “redox reactor” and its edge. The primary reaction initiating the decay of organic matter (TOC max 1620 mg/L, phenol max 613 mg/L) is its aerobic oxidation. In the case of the consumption of free oxygen, the decay undergoes anaerobic oxidation, where the source of electrons are oxides and hydroxides (MnO2, Fe(OH)3). As a result of these reactions, mobile ions Mn2+ and Fe2+ pass into the aqueous environment creating a concentration anomaly (max 15 mg/L for Mn2+, 673 mg/L for Fe2+). The presence of Fe2+ in groundwater is crucial. A strong correlation between the organic matter decay processes and concentration of the Fe2+ showed that “iron index” may be a preliminary marker for the hydrogeochemical recognition of aquifer and allows to diagnose zones with an intense organic matter decay, especially by anaerobic oxidation through redox reactions. At the edge of the “redox reactor” redox sensitive metals (Fe2+, Mn2+ and also Cu2+, Cr3+, Hg2+) undergo aerobic oxidation due to the access of oxygen as a result of mixing of contaminated groundwater and oxygenated pure Quaternary water. These transformations produce oxides and hydroxides (MnO2, Fe(OH)3)—new reaction products, however, are used for anaerobic oxidation of organic matter. Organic matter decay is an cyclic system of redox processes up to the full decay of pollutants and generation of the anomalously high concentrations of redox sensitive metals in the ground.