The release of contaminants such as solvents and other volatile organic compounds (VOCs) into surface impoundment or through other disposal practices has resulted in the contamination of a determined media. These organic contaminants were often introduced to the subsurface as a pure phase that was either lighter than or heavier than water. Those compounds heavier than water, such as solvents, are commonly known as DNAPLs (dense, non-aqueous phase liquids) when they are present as a separate phase. Those compounds lighter than water, such as gasoline, are commonly known as LNAPLs (light, non-aqueous phase liquids) when they are present as a separate phase. DNAPLs and LNAPLs in a media are difficult to remove by pump-and-treat methods, they can be difficult to detect and treat in situ, and act as significant sources of contamination continuously released to the ground water. The chemical substances used in organic synthesis, or in inactivating of biological vaccines, generally are not degraded by conventional wastewater treatment process such as: aerobic, anaerobic treatment or chemical oxidation with chlorine or ozone. The development of Advanced Oxidation Process (AOPs) and Fenton like Process, become a better choice for treating those substances. In this paper, a Fenton Process was performed for treating the residues of the inactivation of microorganisms used for vaccine production and its Quality Control (Potency, sterility, etc.). The yield of the reaction, based on the COD parameter, was very high in all cases. The laboratory scale studies were performed at 25°C with hydrogen peroxide per iron II (ferrous) sulfate ratio of 5. In addition, the studies were performed after an aerobic and an anaerobic biological process. The comparison of all three cases were conducted for the yield, reagent spend and reaction time.