<p>With the intensification of global climate change and the increasing prevalence of eutrophication, harmful algal blooms (HABs) have caused severe environmental damage. Current research predominantly focuses on algal inactivation and remediation, while secondary pollutants such as microcystins (MCs) and algal organic matter (AOM) released after algal lysis also pose significant threats to aquatic ecological security and human health. This review systematically summarizes recent advancements in removal technologies for microcystin-LR (MC-LR) and AOM, emphasizing the mechanisms and efficiencies of coagulation-sedimentation, photocatalysis, Fenton reaction, ultrasonic cavitation, and ozonation. Analysis indicates that integrated coagulation-sedimentation with electrochemical or bio-flocculants achieves high-efficiency algal cell removal and toxin release suppression. Modified photocatalysts enhance carrier separation capacity, enabling rapid MC-LR degradation. Synergistic Fenton and ultrasonic technologies inactivate algal cells and degrade intra/extracellular toxins through interfacial confinement effects and radical chain reactions. Ozone microbubble technology, combining coagulation and oxidation, demonstrates excellent performance in removing cyanobacterial cells and their derivatives as well as eliminating MC-LR. Previous studies and toxicity assessment software have confirmed that hydroxylation of Adda side chains and ring-opening reactions can significantly reduce MC-LR toxicity, though some intermediates may exhibit certain toxicity. This review further highlights the need for future research to prioritize the development of cost-effective integrated technologies with low secondary pollution, improve engineering applicability under complex aquatic conditions, and deepen the analysis of toxicological mechanisms of degradation products, thereby providing theoretical and technical references for the efficient control of MC-LR and AOM.</p> Graphical Abstract <p></p>