This study reports the importance of maintaining a high pH and/or chloramine concentrations in water distribution system to supress the growth of nontuberculous mycobacteria (NTM) - a group containing some opportunistic pathogens. Four sets of reactor systems, each containing three reactors connected in series, were operated at three different feed water pH values (7.6, 8.4, and 9.0) and two different chloramine concentrations (2.6 and 3.8 mg/L). Altogether, 44 operational taxonomic units of NTM were identified. The NTM species Mycobacterium chelonae, M. europaeum, M. gordonae, M. stephanolepidis, M. llatzerense, M. lentiflavum, and M. kyorinense were detected in the majority of the samples. Among them, M. chelonae was highly dominant NTM species in majority of the tested samples. The NTM populations were in the range of 8.83E+ 01–6.30E+ 05 gene copies/mL. Higher relative abundances of NTM were noted in reactors containing higher chloramine residuals, but the number of NTM and total bacterial population increased with the decreasing chloramine concentration, under low pH (<8.4) and under nitrifying conditions. This study underscores the benefits of maintaining high pH in the feed as it not only increases the chloramine stability, but also suppresses the bacterial growth including NTM.