The treatment of toxic Microcystis aeruginosa (M. aeruginosa) by electrolysis using a boron-doped diamond (BDD) anode with a solid polymer electrolyte (SPE) was investigated. In order to examine the role of oxidizing agents, the electrolysis of M. aeruginosa was conducted in distilled deionised water (DIW) with and without sodium chloride aqueous electrolyte. Furthermore, to verify the system's ability for freshwater treatment without the addition of chemicals, we also tested filtered local reservoir water. M. aeruginosa cell inactivation and micro-cystins degradation occurred in the DIW system without a supporting aqueous electrolyte, but cell inactivation occurred at slightly slower rate compared to when 30 mg/L Cl-was added. Even though these rates were even slower in the pre-filtered reservoir water, around 90% inactivation and toxin degradation was still observed after 30 min, and cells were not able to re-grow when subsequently exposed to optimum growth conditions. These results for the first time demonstrate the ability of the SPE system to efficiently treat contaminated freshwaters, even without the addition of chemicals or adjustment of electrical conductivity. Importantly, significant changes in cell morphology after electrolysis in different water matrices were observed. In the DIW with 30 mg/L Cl-test based on the significant differences in oxidants concentrations in the presence and absence of M. aeruginosa suggest that there was a synergistic effect of in situ electro-generated ozone and chlorine species in cell inactivation, however, hydrogen peroxide did not seem to assist in the treatment performance. This study suggests that the electrochemical treatment of BDD with SPE, with and without supporting electrolyte is an effective method for the removal of both toxic cyanobacteria and cyanotoxins.