ABSTRACTNonpigmented and late-pigmenting rapidly growing mycobacteria (RGM) have been reported to commonly colonize water production and distribution systems. However, there is little information about the nature and distribution of RGM species within the different parts of such complex networks or about their clustering into specific RGM species communities. We conducted a large-scale survey between 2007 and 2009 in the Parisian urban tap water production and distribution system. We analyzed 1,418 water samples from 36 sites, covering all production units, water storage tanks, and distribution units; RGM isolates were identified by usingrpoBgene sequencing. We detected 18 RGM species and putative new species, with most isolates beingMycobacterium chelonaeandMycobacterium llatzerense. Using hierarchical clustering and principal-component analysis, we found that RGM were organized into various communities correlating with water origin (groundwater or surface water) and location within the distribution network. Water treatment plants were more specifically associated with species of theMycobacterium septicumgroup. On average,M. chelonaedominated network sites fed by surface water, andM. llatzerensedominated those fed by groundwater. Overall, theM. chelonaeprevalence index increased along the distribution network and was associated with a correlative decrease in the prevalence index ofM. llatzerense, suggesting competitive or niche exclusion between these two dominant species. Our data describe the great diversity and complexity of RGM species living in the interconnected environments that constitute the water production and distribution system of a large city and highlight the prevalence index of the potentially pathogenic speciesM. chelonaein the distribution network.