Peracetic acid (PAA) is a disinfectant considered for use in ballast water treatment, but its chemical behavior in such systems (i.e., saline waters) is largely unknown. In this study, the reactivity of PAA with halide ions (chloride and bromide) to form secondary oxidants (HOCl, HOBr) was investigated. For the PAA-chloride and PAA-bromide reactions, second-order rate constants of (1.47 ± 0.58) × 10(-5) and 0.24 ± 0.02 M(-1) s(-1) were determined for the formation of HOCl or HOBr, respectively. Hydrogen peroxide (H2O2), which is always present in PAA solutions, reduced HOCl or HOBr to chloride or bromide, respectively. As a consequence, in PAA-treated solutions with [H2O2] > [PAA], the HOBr (HOCl) steady-state concentrations were low with a limited formation of brominated (chlorinated) disinfection byproducts (DBPs). HOI (formed from the PAA-iodide reaction) affected this process because it can react with H2O2 back to iodide. H2O2 is thus consumed in a catalytic cycle and leads to less efficient HOBr scavenging at even low iodide concentrations (<1 μM). In PAA-treated solutions with [H2O2] < [PAA] and high bromide levels, mostly brominated DBPs are formed. In synthetic water, bromate was formed from the oxidation of bromide. In natural brackish waters, bromoform (CHBr3), bromoacetic acid (MBAA), dibromoacetic acid (DBAA), and tribromoacetic acid (TBAA) formed at up to 260, 106, 230, and 89 μg/L, respectively for doses of 2 mM (ca. 150 mg/L) PAA and [H2O2] < [PAA]. The same brackish waters, treated with PAA with [H2O2] ≫ [PAA], similar to conditions found in commercial PAA solutions, resulted in no trihalomethanes and only low haloacetic acid concentrations.