Poor drinking water quality can affect pigs’ health and performance. The disinfection of water may enhance microbial water quality. In this study, bacteria and endotoxins in sodium hypochlorite-treated and -untreated water from one pig nursery were analyzed. Water samples were taken from incoming water and from compartments with treated and untreated water at the beginning and end of pipes and from nipples. The farm was visited 14 times to measure total bacteria counts and concentrations of Pseudomonas spp. and endotoxins. Additionally, the occurrence of coliform bacteria was analyzed. A mixed model analysis revealed significant reductions in total bacteria counts and Pseudomonas spp. in treated water at the beginning of pipes and at nipple drinkers. The differences between bacteria concentrations at the end of pipes had no clear trend. Endotoxin concentrations were approximately equal at the beginning of pipes and at nipple drinkers but were found to have differences at the end of pipes. The occurrence of coliform bacteria was significantly reduced in treated water. The application of sodium hypochlorite can significantly reduce bacteria in water pipes. Endotoxin concentrations were mostly unaffected by water treatment. Disinfection of the dead-end pipe sections failed, and thus these parts should be regarded as potential contamination sources.