Microcystin-LR (MC-LR) and cylindrospermopsin (CYN) are toxic cyanotoxins frequently found in drinking water sources, posing significant health risks. This study conducted a microcosm experiment using surface lake water exposed to sunlight to investigate the natural attenuation processes of MC-LR and CYN. Results indicated that photodegradation plays a crucial role in the natural attenuation of cyanotoxins. The half-lives of MC-LR and CYN were 1 and 7 days in summer under a combined effect of direct and indirect photodegradation, respectively. The effectiveness of these natural processes varied seasonally, with faster dissipation rates observed during summer. Bacterial degradation notably affected only MC-LR in summer, with a negligible effect on CYN. The identified transformation products showed that the conversion of MC-LR involved oxidation, hydroxylation, and/or bond cleavage with Adda and Mdha moieties, while it entails the oxidation of the tricyclic guanidine moiety and opening of the uracil ring for CYN. The Ames assay confirmed that these transformation products from the natural attenuation of MC-LR and CYN did not induce genotoxicity or mutagenicity. While these findings enhance our understanding of natural attenuation mechanisms, they also offer valuable insights that could guide artificial control strategies or improve the efficiency of cyanotoxin management. However, natural degradation processes alone, particularly in large water bodies, may be insufficient to fully mitigate cyanotoxin risks, highlighting the continued need for comprehensive management approaches.