Estuarine water treated with a ballast water management system (BWMS) using a solution of dissolved dichloroisocyanurate dihydrate (DICD) resulted in the formation of newly described brominated disinfection by-products (Br-DBPs). Analysis of dissolved organic matter (DOM) in untreated water with ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) identified 3897 m/z ions and their exact molecular formulas. After DICD treatment, a total of 213 halogenated molecular ions with relative abundance of at least 1% were assigned and confirmed using isotope simulation. Halogenated ions were assigned in four DBP elemental groups including CHOBr (180), CHONBr (13), CHOCl (16), and CHOBrCl (4). Forty-nine of the 197 brominated formulas have not been previously reported. We also were able to tentatively assign possible structures to the formula C3Br3N2 due to very limited isomeric possibilities. The tentatively assigned compound found at 6.4% relative abundance was identified as either tribromoimidazole or tribromopyrazole. Our results show the formation of complex halogenated DBPs that are formed in the treatment of water with a novel BWMS that employs granular DICD as a biocide. The toxicological and mutagenic properties as well as the fate of these newly identified brominated DBPs are unknown.