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The application of non-thermal plasmas in wastewater and air purification received a lot of attention, but their potential application in drinking water treatment has scarcely been investigated. Classified as Advanced Oxidation Processes, plasmas ignited in water or at the air-water interface generate a vast range of reactive species capable of removing water contaminants. The efficiency to degrade cylindrospermopsin (CYN, cyanobacterial toxin) was compared for six different plasma sources. A spark discharge showed the most energy-efficient degradation, followed by the other investigated systems, which showed similar trends. Two approaches were selected for further in-depth study of the degradation efficiency and underlying mechanisms. For a follow-up detailed study, a corona-like and a dielectric barrier discharge were selected based on the CYN degradation efficiency, usability of the reactors and plasma-chemistry. For the corona-like plasma, the degradation efficiency increased with increasing voltage and solution pH. After 15 min of plasma treatment at pH ≥ 7.5, degradation of CYN even progressed without further plasma application. The pH-dependency was not observed for the dielectric barrier discharge (DBD), whose degradation efficiency increased with decreasing operating voltage. The corona-like plasma promotes degradation primarily via OH, whereas the DBD produces mainly O3 and NOx. The application of non-thermal plasmas (NTPs) appears to be an innovative and promising approach for effective removal of cyanotoxins such as cylindrospermopsin from drinking water.