In literature, the microbial diversity of hot spring waters has been the focus of extensive research, while there is a paucity of studies on thermal water distribution network of spa centres and as yet no studies have been carried out on the bacterial population of thermal muds. In this context, the aim of our study is to characterize the microbial community of sulphurous-bromine-iodine thermal water and mud within an Italian spa complex using Next Generation Sequencing (NGS) technologies. This is the first report of microbiome characterization along a water supply network from the spring to points of use within a spa. According to the 16S rRNA gene sequences analysis, our data highlight the presence of a typical microbial community, mainly composed of sulphur-cycling bacteria belonging to Desulfomonile, Thermodesulfovibrio, Geothermobacterium, Thermus, Thiofaba and Syntrophomonas genera. In addition, the characterization and evolution of the bacterial community in thermal muds during the maturation process is investigated for the first time. Interestingly, the microbiome of mature mud resulted dominated by bacteria capable of lipid biosynthesis, suggesting that these bacteria may play a role in the anti-rheumatic properties of thermal mud.