The decomposition of hydrogen peroxide catalyzed by iron and copper leads to the generation of reactive oxidants capable of oxidizing various organic compounds. However, the specific nature of the reactive oxidants is still unclear, with evidence suggesting the production of hydroxyl radical or high-valent metal species. To identify the reactive species in the Fenton system, the oxidation of a series of different compounds (phenol, benzoic acid, methanol, Reactive Black 5 and arsenite) was studied for iron- and copper-catalyzed reactions at varying pH values. At lower pH values, more reactive oxidants appear to be formed in both iron and copper-catalyzed systems. The aromatic compounds, phenol and benzoic acid, were not oxidized under neutral or alkaline pH conditions, whereas methanol, Reactive Black 5, and arsenite were oxidized to a different degree, depending on the catalytic system. The oxidants responsible for the oxidation of compounds at neutral and alkaline pH values are likely to be high-valent metal complexes of iron and copper (i.e., ferryl and cupryl ions).