Iron(II) is oxidized by hydrogen peroxide to iron(III), forming a hydroxyl radical and a hydroxide ion in the process. Iron(III) is then reduced back to iron(II) by another molecule of hydrogen peroxide, forming a hydroperoxyl radical and a proton. The net effect is a disproportionation of hydrogen peroxide to create two different oxygen-radical species, with water (H + OH) as a byproduct. 
The free radicals generated by this process engage in secondary reactions. For example, the hydroxyl is a powerful, non-selective oxidant. Oxidation of an organic compound by Fenton's reagent is rapid and exothermic and results in the oxidation of contaminants to primarily carbon dioxide and water. 
Reaction () was suggested by Haber and Weiss in the 1930s as part of what would become the Haber–Weiss reaction.
Iron(II) sulfate is typically used as the iron catalyst. The exact mechanisms of the redox cycle are uncertain, and non-OH oxidizing mechanisms of organic compounds have also been suggested. Therefore, it may be appropriate to broadly discuss Fenton chemistry rather than a specific Fenton reaction.
In the electro-Fenton process, hydrogen peroxide is produced in situ from the electrochemical reduction of oxygen.
Fenton's reagent is also used in organic synthesis for the hydroxylation of arenes in a radical substitution reaction such as the classical conversion of benzene into phenol.
An example hydroxylation reaction involves the oxidation of barbituric acid to alloxane. Another application of the reagent in organic synthesis is in coupling reactions of alkanes. As an example tert-butanol is dimerized with Fentons reagent and sulfuric acid to 2,5-dimethyl-2,5-hexanediol. Fentons reagent is also widely used in the field of environmental science for water purification and soil remediation. Various hazardous wastewater were reported to be effectively degraded through Fenton's reagent.