The microbiological monitoring of mineral bottled waters results is crucial for the prevention of outbreaks in consumers. European and International regulations establish the quality of water intended for human consumption in order to preserve human health from the negative effects deriving from water contamination. Advanced methods targeting the faster detection of potential pathogens in drinking water may consent to the creation of an early warning system, enhancing water quality management. This study aimed to suggest the implementation of standard water quality evaluations, based on the characterization of the microbial composition of mineral bottled water brands, contributing to the periodic control of the water’s microbiological stability along with the shelf life, and, consequently, the stability of the supplying sources. Bottled water microbiota analysis was combined with the qualitative and quantitative evaluation of microbial loads in time, and the monitoring was performed in two seasons and two different storage conditions for a total of sixty days. The employment of molecular microbiology techniques (NGS and Sanger sequencing), compared to standardized cultural methods and integrated with metagenomic analysis, combining chemical and physical indicators for each sample, allowing for the generation of specific fingerprints for mineral bottled waters, pointing at simplifying and improving the foreseen risk assessment strategies to ensure the adequate traceability, quality and safety management of drinking water.