In contrast to pathogens, the effects of environmental microbes on the water quality in baths have not yet been examined in detail. We herein focused on a public bath in which groundwater was pumped up as bath water and disinfected by chlorination. Ammonia in groundwater is oxidized to nitrite, thereby reducing residual chlorine. A batch-culture test and bacterial community analysis revealed that ammonia-oxidizing bacteria accumulated nitrite and had higher resistance to chlorination than nitrite-oxidizing bacteria. These results demonstrate that the difference in resistance to chlorination between ammonia-oxidizing and nitrite-oxidizing bacteria may lead to the accumulation of nitrite in baths using groundwater.