Total organic halogen (TOX) is widely used as a surrogate bulk parameter to measure the overall exposure of halogenated disinfection byproducts (DBPs) in drinking water. In this study, we surprisingly found that the level of TOX in chlorinated waters had been significantly underestimated under common analytical conditions. After the addition of quenching agent sodium thiosulfate, total organic chlorine and total organic bromine exhibited a two-phase decomposition pattern with increasing contact time, and a significant decomposition was observed for different types of quenching agents, quenching doses, and pH conditions. More importantly, the decomposed TOX closely correlated with the acute toxicity of quenched water against luminous bacteria, implying that the DBPs responsible for TOX decomposition could be of important toxicological significance. Based on nontarget analysis by using high-resolution mass spectrometry, molecular formulas for the decomposed TOX were determined. After re-examining the mass balance of TOX in the context of unintentional decomposition, it was found that both the level and percentage of unknown TOX in chlorinated waters were considerably higher than historically thought. Overall, this study brings new insights into the knowledge of TOX formed during chlorination, providing important clues on the identification of toxicity driver in drinking water.