Microcystins (MC) and cylindrospermopsin (CYN) are potent toxins produced by diverse cyanobacterial genera found in waterbodies throughout the world. In the present study, and in order to achieve a better understanding of the fate of cyanobacterial toxins in the environment, we assessed the photodegradation of MC and CYN along the water column and by different radiation bands of the natural solar spectrum: photosynthetic active radiation (PAR), UV-A, and UV-B. Photodegradation of CYN seemed to be highly dependent on UV-A and was very low under natural conditions. This fact could be one of the reasons explaining the high extracellular CYN concentration found in diverse waterbodies. Microcystin photodegradation was higher, all three radiation bands (PAR, UV-A, and UV-B) being responsible for its degradation, although PAR and UV-A were more efficient because of their high natural irradiance. Modeling of MC photodegradation along the watercolumn was performed, using specific MC breakdown rates for the different radiation bands and including calculated attenuation coefficients for these bands. As a result, we suggest that rapid and efficient MC photodegradation may be expected in shallow systems or thin mixed layers.