Rising global temperatures and nutrient pollution are responsible for the rising occurrence of harmful cyanobacterial blooms. These blooms are responsible for hepato- and neuro-toxins that pose threats to human and animal health. The cyanobacterium Microcystis aeruginosa is a  common freshwater cyanobacteria responsible for producing hepatotoxins termed microcystins. Microcystin-LR (MC-LR) is the most prevalent and most toxic. Studies were performed to 1) understand the response of the cyanotoxin-producing cyanobacterium to electron beam (eBeam) doses, 2) understand the susceptibility of the microcystin-LR molecule to varying electron beam doses, 3) understand the expression of the cyanobacterial genes as a function of eBeam dose and 4) determine whether eBeam doses are effective at degrading microcystin-LR in surface waters from different geographical regions. The results indicate that low doses of eBeam treatment (<400 Gy) are sufficient to degrade MC-LR at environmentally relevant concentrations. eBeam doses >2 kGy were sufficient to prevent M. aeruginosa cell growth and induced cell lysis with a delay of approximately 2 hours following eBeam exposure. Surface water samples from 22 locations across the US were spiked with defined concentration of MC-LR (3 mg/L) and exposed to 5 kGy eBeam dose. The results indicate that the 5 kGy eBeam dose was able to degrade >99% of MC-LR in these samples regardless of their water chemistry. In terms of gene expression responses, there was distinct clustering between gene expression patterns and dose. Genes associated with photosynthesis and biosynthesis were down regulated at 2 kGy and 5 kGy. These biological responses mirror the responses observed in metabolically active yet non culturable bacterial cells.