Ozonation is widely used during water treatment but can generate a variety of toxic disinfection byproducts, especially in the presence of bromide. In the present study, our halogen extraction code was extended and modified to identify bromine isotopic patterns and combined with the R package MFAssignR in selectively identifying brominated disinfection byproducts (Br-DBPs) from high resolution mass spectra. In total, 127 Br-DBPs formed from a Suwannee River natural organic matter (SRNOM) solution were successfully detected from tens of thousands of mass spectrometry peaks. Kendrick mass defect analysis and structural characterization identified 17 structures, 15 of which were identified as brominated carboxylic acids and firstly reported here. Computational model predictions indicated that these brominated carboxylic acids may possess high toxic potencies and raise valid concerns. The adapted halogen extraction code described in this study is a powerful tool for a wider application of analyzing Br-DBPs in complex water matrices and provides an effective technique to characterize and identify these compounds in future studies.