Microcystin-LR (MC-LR), a cyanotoxin produced during some harmful algal blooms (HABs), can have negative impacts on water ecosystems. Current treatment methods have potential drawbacks: physical removal can cause cell lysis and toxin release, and chemical treatment can cause disinfection byproducts (DBPs). Ultraviolet C (UV-C) treatment can degrade cyanotoxins without producing additional waste in the process. In this study we compared the degradation of MC-LR (initial concentration ~50 ppb) in deionized (DI) water and surface waters by UV-C light emitted from a krypton-chlorine excimer lamp (UV222) versus a low-pressure Hg lamp (UV254). Quantitative analyses of the resulting samples by protein phosphatase 2a (PP2a) inhibition assays and liquid chromatography-high resolution mass spectrometry (LC-HRMS) were completed. The results of these analysis are provided in this data release.