A johkasou system is getting popular as a decentralized wastewater treatment system in low-density communities. Treated waters of the johkasou systems, which are generally discharged into channels within residential areas before entering the local receiving water body, may contain microbial contaminants. To identify the characteristics of fecal indicators in the channels of the johkasou systems, the concentrations of fecal indicators (F-RNA bacteriophages, GIII F-RNA bacteriophages, Escherichia coli, and total coliforms) were examined both in water and sediment in the channels of three johkasou systems. These fecal indicators were always detected at high levels both in water and sediment in the channels of three johkasou systems through the study period. Significant differences in concentrations of fecal indicators were not observed among three johkasou systems in different residential areas. Concentrations of fecal indicators fluctuated in a day mainly due to domestic activities. Significant positive correlations of total coliforms and E. coli in water with total coliforms and E. coli in sediment suggest the potential importance of sediment on microbial dynamics in the channels of the johkasou systems. No significant correlations of F-RNA bacteriophages with total coliforms and E. coli indicate a specific distribution mechanism for F-RNA bacteriophages.