In this paper, certain investigations were performed in the following aspects: analysis of optical emission spectra which is used for the identification of ˙OH, ˙H, ˙O, H2O2 and O3 on the inactivation of algae by observing the gas and liquid phase compositions, the optimal parameters such as treatment time, pulse peak voltage, and pulse frequency. Each experiment was carried out by introducing two difference gases, oxygen or air, separately above the liquid in the reactor. The results showed that the inactivation rate of algae reached 100% in the case of oxygen bubbling into the Chlorella spp. contaminated water for 7 min and the Chrysophyta spp. for 5 min. It took much longer time in the case of air bubbling that took 10 min for Chlorella spp. and 7 min for Chrysophyta spp.