Algal organic matter (AOM), a significant source of endogenous dissolved organic matter (DOM) is released in high concentrations during cyanobacterial blooms, along with cyanotoxins. Subsequent photobleaching of AOM is an important phenomenon to investigate. In this study, intracellular organic matter (IOM) and extracellular organic matter (EOM) were extracted from cultured cyanobacteria taken from Taihu Lake in China. The formation of photochemically produced reactive intermediates in different stages of IOM and EOM photobleaching was compared to Suwannee River DOM (SRDOM, reference standard DOM). Results revealed notable differences influenced by the pigment component among IOM, EOM, and SRDOM. The pigment in IOM contributed to a triplet state pool with strong energy-transfer but limited electron-transfer capabilities. Notably, IOM exhibited the highest triplets state quantum yield value in the visible region, suggesting its potential significance in pollutant degradation in deeper water layers. For EOM, one of the pools exhibits photolability and remarkable electron-transfer capability, indicating it as a high-energy triplet state component. Moreover, three cyanotoxins (MC-LR, ACA, and ATX-a) were detected in the extracted AOM, and their photodegradation was monitored during the AOM photobleaching process. This highlights the potential role of AOM as a photosensitizer in the natural self-cleaning mechanisms of water bodies, facilitating the degradation of organic pollutants through photochemical reactions. The findings of this study contribute to understanding the dynamic nature of AOM and its implications in environmental processes.