Microcystins (MCs) produced by cyanobacteria are strong hepatotoxins and classified as possible carcinogens. MCs pose a considerable threat to consumers of tainted drinking and surface waters, but the photochemical fate of dissolved MCs in the environment has received limited attention. MCs are released into the environment upon cell lysis along with photoactive pigments including phycocyanin and chlorophyll a. The concentrations of MCs and pigments are expected to be greatest during a bloom event. These blooms occur in sunlit surface water and thus MCs can undergo a variety of solar initiated or photosensitized transformations. We report herein the role of oxygen, sensitizer, and light on the photochemical fate of MCs. The phycocyanin photosensitized transformation of MCs is elucidated, and photosensitized isomerization plays an important role in the process. The UV-A portion of sunlight was simulated using 350 nm light and the phototransformations of three MC variants (-LR, -RR, -LF) were investigated. Singlet oxygen leads to photooxidation of phycocyanin, the predominant pigment of cyanobacteria, hence, reducing the phototransformation rate of MCs. The phototransformation rate of MC-LR increases as pH decreases. The pH effect may be the result of MCs association with phycocyanin. Our results indicate photosensitized processes may play a key role in the photochemical transformation of MCs in the natural water.