DDue to its widespread presence in groundwater, nitrate contamination has become a major global concern. Identifying the different sources of this contamination, particularly those related to agricultural practices, is therefore crucial to assess its negative impacts. The European Nitrates Directive (91/676/EEC) requires the protection of all natural freshwater resources with a maximum nitrate concentration threshold of 50 mgNO3+L-1, applicable to all groundwater, regardless of its intended use. Many studies have used a chemical approach to identify these contaminations, but one of the possible approaches to identify contamination and the source of the contamination is a microbiological approach. An aquifer's unique groundwater fingerprint: its hydrology, chemistry, and geology are shaped by the communities of heterotrophic bacteria that thrive in this underground environment. The present study carries out an evaluation of the impact of nitrate and ammonia on the bacterial community of groundwater, in particular by studying the correlations between the two chemical forms analyzed and some of the native species most present in nitrifying and denitrifying groundwater. These evaluations make it possible to identify the microbial species subject to the variation of ammonia and nitrate concentrations and to evaluate the extent of variation in the natural environment, providing useful information on the variation of the chemical compound, validating the innovative thesis of being used as a natural tracer for the identification of potential direct or indirect contamination.