As well established in the literature, residual toxicity is an important parameter for evaluating the sanitary and environmental safety of water treatment processes, and this parameter becomes even more crucial when chlorine-based processes are applied for water treatment. Eliminating initial toxicity or preventing its increase after water treatment remains a huge challenge mainly due to the formation of highly toxic disinfection by-products (DBPs) that stem from the degradation of organic contaminants or the interaction of the chlorine-based oxidants with different matrix components. In this review, we present a comprehensive discussion regarding the toxicological aspects of water treated using chlorine-based advanced oxidation processes (AOPs) and the recent findings related to the factors influencing toxicity, and provide directions for future research in the area. The review begins by shedding light on the advances made in the application of free chlorine AOPs and the findings from studies conducted using electrochemical technologies based on free chlorine generation. We then delve into the insights and contributions brought to the fore regarding the application of NH2Cl- and ClO2-based treatment processes. Finally, we broaden our discussion by evaluating the toxicological assays and predictive models employed in the study of residual toxicity and provide an overview of the findings reported to date on this subject matter, while giving useful insights and directions for future research on the topic.