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With accumulating evidence of pulmonary infection via aerosolized nontuberculous mycobacteria (NTM), it is important to characterize their persistence in wastewater treatment, especially in arid regions where treated municipal wastewater is extensively reused. To achieve this goal, microbial diversity of the genus Mycobacterium was screened for clinically and environmentally relevant species using pyrosequencing. Analysis of the postdisinfected treated wastewater showed the presence of clinically relevant slow growers like M. kansasii, M. szulgai, M. gordonae, and M. asiaticum; however, in these samples, rapid growers like M. mageritense occurred at much higher relative abundance. M. asiaticum and M. mageritense have been isolated in pulmonary samples from NTM-infected patients in the region. Diversity analysis along the treatment train found environmentally relevant organisms like M. poriferae and M. insubricum to increase in relative abundance across the chlorine disinfection step. A comparison to qPCR results across the chlorine disinfection step saw no significant change in slow grower counts at CT disinfection values <= 90 mg.min/L; only an increase to 180 mg.min/L in late May brought slow growers to below detection levels. The study confirms the occurrence of clinically and environmentally relevant mycobacteria in treated municipal wastewater, suggesting the need for vigilant monitoring of treated wastewater quality and disinfection effectiveness prior to reuse.