During chlorination of seawater, the presence of bromide and ammonia alters the speciation of the oxidant and lead to the formation of chlorinated and brominated amines. This can affect the effectiveness of the disinfection treatment and the formation of disinfection by-products released to the environment. In this study, a Membrane Introduction Mass Spectrometry (MIMS) analytical method was developed to differentiate brominated trihalamines (i.e. tribromamine NBr3, dibromochloramine NBr2Cl and bromodichloramine NBrCl2) in synthetic and natural chlorinated seawater. A mass-to-charge ratio of m/z = 253 corresponding to the parent ion was used for the quantification of NBr3 in absence of organic matter and the signal of the fragment at m/z = 177 was chosen in presence of high concentration of organic matter. Limits of detection were 0.23 μM (49 μg Cl2/L) and 0.18 μM (38 μg Cl2/L) for m/z 253 and m/z 177, respectively. Both NBr2Cl and NBrCl2 were monitored in chlorinated seawaters with their respective parent ion at m/z = 207 and m/z = 163 but were not quantified. MIMS results also showed that reaction of brominated trihalamines with natural organic matter (NOM) was a minor pathway for 1–2 mg C/L compared to their auto-decomposition in natural or synthetic seawater. Overall, MIMS was able to unambiguously differentiate and monitor brominated trihalamines for the first time in chlorinated seawater, which was not possible by using UV measurement, titration and colorimetric methods.