Background Cyanobacteria and their toxins occur in high concentrations during the so-called bloom events in surface waters. To be able to assess the risks associated with cyanobacterial blooms, we need to understand the persistence and fate processes of these toxins and other bioactive metabolites. In this study, we investigated the photochemical fate of 54 cyanopeptides extracted from two strains of Microcystis aeruginosa (PCC7806 and UV006), Planktothrix rubescens, and Dolichospermum flos aquae. We determined half-lives during sunlight exposure in lake water and inspected the effect of pH on transformation kinetics for 27 microcystins, 8 anabaenopeptins, 14 cyanopeptolins, 2 cyclamides, and 3 aeruginosins. Results For cyanopeptides from D. flos aquae and P. rubescens, we observed the highest removal of 28 and 26%, respectively, after 3-h sunlight exposure. Most cyanopeptides produced by the two M. aeruginosa strains were rather persistent with only up to 3% removal. The more reactive cyanopeptides contained amino acids known to undergo phototransformation, including methionine and tyrosine moieties or their derivatives. Photochemical half-lives of 14 tyrosine-containing cyanopeptides decreased by one order of magnitude from nearly persistent conditions at pH 7 (half-life > 70 h) to shorter half-lives at pH 10 (< 10 h). Conclusions More work is needed to distinguish the contribution of different photochemical reaction pathways including the contributions to the pH effect. To the best of our knowledge, this is the first assessment of transformation kinetics of such a wide range of cyanopeptides. The abundant and persistent cyanopeptides that have not been studied in detail yet should be prioritized for the evaluation of their ecosystem and human health risks and for their abatement during drinking water treatment.