Abstract Passive co-treatment of municipal wastewater and synthetic acid mine drainage in a laboratory-scale, four-stage continuous flow reactor system was examined for changes in fecal indicator bacteria (FIB) counts. Raw municipal wastewater (MWW) from the City of Norman, Oklahoma was mixed at a 2:1 ratio with high-strength synthetic acid mine drainage and introduced to the system. The MWW contained varying concentrations of total coliforms (TC), fecal coliforms (FC), Escherichia coli, and fecal streptococci (FS). Initial concentrations ranged from 6 to 13, 0.6 to 6, 3 to 5, and 0.1 to 0.7 million cfu/100 mL, for TC, FC, E. coli, and FS, respectively. During the 6.6-day system residence time, a 100% reduction of all FIB was observed. However, FIB exhibited evidence of sub-lethal injury with slower colony formation rates on standard growth media after 81 h of retention. Extending standard incubation periods resulted in higher concentrations of all FIB in each treatment stage, except the final stage where only E. coli and TC counts increased. Although this co-treatment regime reduced FIB concentrations more effectively than conventional active or passive MWW treatment systems, further work can be done to optimize the efficiency of treating these wastes simultaneously.