Non-tuberculous mycobacteria (NTM) are ubiquitous environmental organisms that can cause severe infections in vulnerable individuals. However, the environmental reservoirs and transmission routes of clinically relevant NTM remain insufficiently understood. Given the rising incidence of NTM infections, understanding where these bacteria thrive can inform public health measures and reduce infection risk. In this study, we analysed the prevalence and genetic diversity of mycobacteria in indoor water samples from private residences and a hospital in Frankfurt am Main, Germany, and characterised them using whole genome sequencing and phenotypic drug susceptibility testing. Core genome multi-locus sequence typing (cgMLST) was employed to compare environmental isolates with nearly 3,000 clinical and environmental NTM isolates from around the world, aiming to identify potential epidemiological connections and global lineages. NTM were isolated from 9 of 41 households (22.0%) and 15 of 102 water samples (14.7%). Eight different NTM-species were identified, including one novel species. For Mycobacterium abscessus and Mycobacterium chimaera, strains belonging to globally distributed lineages were detected. Notably, M. abscessus dominant circulating clone 3 (DCC3) was present in shower water and we report, for the first time, global lineages of M. chelonae in both environmental and clinical samples. While NTM from different households were genetically distinct, isolates from five households (M. chimaera, M. abscessus, and M. chelonae) were closely related to clinical isolates from Germany and abroad. In conclusion, our findings highlight indoor water systems as reservoirs for some clinically significant NTM, including globally relevant clones such as M. abscessus DCC3, and underscore the potential for targeted public health interventions to reduce exposure risks, especially for vulnerable populations.