Removal of phatogenic bacteria from water by radio-frequency thermal plasma treatment was investigated using three different sizes of reactors and three different applied frequencies in batch experiments. The sources of the water samples were river water, groundwater and mountain water. The results show that the removal efficiency (RE) of total coliforms was 86, 91 and 100% for river water, groundwater and mountain water, respectively, after a 20-minute treatment in a radio-frequency (RF) plasma reactor with a diameter of 2 inch and an applied frequency of 3.7 MHz. Compared to total coliforms, the RE of fecal coliforms was 91, 100 and 100% for river water, ground water and mountain water, respectively. The RE of total coliforms and fecal coliforms increased with an increase of the frequency or with a decrease of the diameter of the reactor. Increasing the frequency or decreasing the diameter of the reactor caused a decline in the death yield of phatogenic bacteria (CFU/kW h). Based on these results, the removal of phatogenic bacteria from water by RF thermal plasma treatment could be a viable alternative process for decontaminating drinking water in the future.