Thermal springs are natural environments present all over the world and their use represents a social-economical resource with an impact on sanus per aquam (SPA) medical and wellness applications. Physical-chemical and microbiological balances characterize these ecological niches and their knowledge is essential to define water properties and support appropriate management. This study is a pilot application of a larger research project, involving metagenomics and aimed to fingerprint springs and map SPA biodiversity. Waters and their deposits were collected in six thermal springs from the Lazio region in Italy. The phylogenic microbial profiles performed by Next Generation Sequencing (NGS) analysis showed a clear separation between different springs. Statistical analyses revealed correlations between the abundance of specific bacteria and environmental variables. Temperature, Sodium and H2S levels appear to play a key role in influencing the microbiota. The extension of this model to other springs will contribute to characterize and map the microbial community in thermal springs, allowing associations with chemical-physical factors. Biodiversity is a still underestimated property of thermal springs and a key element in several SPA applications. The Atlas progress is shedding light on biotic and abiotic components in these ecological niches, opening further perspectives for supporting appropriate use and management of thermal waters.