This study aims to evaluate the effects of Fe2+ present in carbonated natural mineral waters on the decomposition of hydrogen peroxide (H2O2) used as sanitizing agent of the collector water tanks and the oxidation of NH4+ to NO3– and NO2– nitrogen compounds from bottled carbonated natural mineral water by the Fenton process. This evaluation suggests that the distribution of the nitrogen compounds, at certain concentrations of H2O2 is influenced by facilitated Fenton reaction in the presence of natural Fe2+ ions. Based on the impact of sanitizing agent, which generates in-situ Fenton system, the variations of the NO3– and NO2– were monitored as a result of the complex matrices. The obtained results lead to first conclusion about the possible modifications in the chemical composition of natural mineral waters in the presence of traces of H2O2.