Advanced oxidation using UV/free chlorine and UV/chloramines are being considered as alternatives to UV/H2O2 for treatment of reverse osmosis (RO) permeate in treatment trains for the potable reuse of municipal wastewater. This pilot-scale comparison of the three advanced oxidation processes (AOPs) evaluated three factors important for selecting among these alternatives. First, the study characterized the speciation of oxidants serving as the source of radicals within the AOPs to facilitate process modeling. Kinetic modeling that included consideration of the chloramines occurring in RO permeate accurately predicted oxidant speciation. Modeling of the UV/free chlorine AOP indicated that free chlorine is scavenged by reactions with ammonia and monochloramine in RO permeate, such that oxidant speciation can shift in favor of dichloramine over the short (∼30 s) timescale of AOP treatment. Second, the order of efficacy for degrading the target contaminant, 1,4-dioxane, in terms of minimizing UV fluence was UV/free chlorine > UV/H2O2 ≫ UV/chloramines. However, estimates indicated that the UV/chloramines and UV/H2O2 AOPs could be similar on a cost-effectiveness basis due to savings in reagent costs by the UV/chloramines AOP, provided the RO permeate featured >3 mg/L as Cl2 chloramines. Third, the study evaluated whether the use of chlorine-based oxidants within the UV/free chlorine and UV/chloramines AOPs enhanced disinfection byproduct (DBP) formation. Even after AOP treatment and chloramination, total halogenated DBP formation remained low at <15 μg/L for all three AOPs. DBP formation was similar between the AOPs, except that the UV/free chlorine AOP promoted haloacetaldehyde formation, while the UV/H2O2 and UV/chloramines AOPs followed by chloramination increased chloropicrin formation. However, total DBP formation on a toxic potency-weighted basis was similar among the AOPs, since haloacetonitriles and haloacetamides were the dominant contributors and did not differ significantly among the AOPs.