Cylindrospermopsin (CYN) is a potent toxic alkaloid produced by a number of cyanobacteria frequently found in lakes and reservoirs used as drinking water sources. We report for the first time detailed pathways for the degradation of CYN by treatment with ozone. This was accomplished by use of ultra-high-performance liquid chromatography (UHPLC)-quadrupole time-of-flight mass spectrometry (QTOF MS), which revealed that CYN is readily degraded by ozone with at least 36 transformation products. Structural similarities among the major products indicated that the carbon-carbon double bond in the uracil ring of CYN was most susceptible to attack by ozone. Furthermore, the nitrogen functionality associated with the tricyclic guanidine moiety is also involved via a degradation pathway that has not been previously observed. To assess the potential toxicity of ozonation products of CYN, the cytotoxicity of CYN and the mixture of its ozonation products was measured in a human hepatoma cell line (HepG2). The IC50 for CYN at 24 and 48 h incubations was approximately 64.1 and 12.5 μM, respectively; however, the ozonation products of CYN did not exhibit measurable cytotoxicity to human cells. The results indicate ozone is an effective and practical method for CYN attenuation in water treatment without formation of overtly toxic transformation products.