Halobenzoquinones (HBQs) are a novel family of unregulated disinfection byproducts (DBPs). Little is known about their phototransformation activities in natural water. Here, five HBQs with various halogenated substituent types, numbers, and structures positions were selected to investigate the kinetics of degradation in aqueous solutions at various concentrations and in the presence of common environmental variables (Cl−, NO2−, and humic acid). The results indicated that dichloride and dibromo-substituted HBQs were photolyzed, whereas tetrachloro-substituted HBQs showed little degradation. The photolysis rate constant (k) of HBQs decreased with increasing initial concentration. The presence of NO2− and Cl− promoted the degradation of HBQs mainly through the formation of hydroxyl radical (•OH), which were confirmed by electron paramagnetic resonance (EPR). In contrast, humic acid played a negative role on HBQs transformation due to the adsorption and quenching reactions. Possible conversion pathways for HBQs were proposed based on the identification of two major photodegradation products, hydroxylated HBQs and halogenated-benzenetriol, as well as reactive free radicals. This study provided meaningful insights into the environmental fates and risk assessments of HBQs in natural aquatic system.