Intermittently operated distribution systems serve over one billion people and may be impacted by the intrusion of contaminated waters carrying disinfection byproduct (DBP) precursors. The impact of intrusion on the formation of 19 DBPs was evaluated in an intermittent water system supplied by deep aquifers in Dhaka, Bangladesh. Untreated piped water samples were collected from residential taps and chlorinated under controlled conditions. Chloride, dissolved organic carbon, and the artificial sweetener sucralose were measured as indicators of intrusion. Most piped water samples had low concentrations of DBPs and indicators; however, a subset had higher levels of DBPs and indicators, suggesting the intrusion of contaminated water into the distribution system, particularly during the rainy season. Piped water samples with evidence of intrusion typically formed higher concentrations of haloacetaldehydes and haloacetonitriles when chlorinated, which greatly increased the calculated cytotoxicity. DBP formation and calculated cytotoxicity in piped water samples impacted by intrusion were comparable to those in piped water samples supplied by horizontal and vertical recharge-impacted groundwaters, yet lower than piped surface waters from other regions of Dhaka. The results demonstrated that intrusion can increase DBP formation in an unpredictable fashion, highlighting the need to sample from many locations in intermittent water systems to accurately evaluate DBP exposure risk.