Disinfection of water and water resources from E. coli pathogenic bacteria using high voltage electric pulse treatment is studied. The methods of determination of concentration of microorganisms prior to and after the pulse treatment process are shown. The experimental results are presented on the effect of different modes of the treatment (crown, electric spark discharges), the period of the treatment (the number of discharges), the electric parameters of a high voltage generator (voltage, polarity, charging capacitance), and the initial concentration of microorganisms on changes in their quantity after the electric pulse impact. It was found that the degree of inactivation depends greatly on the mode and time of treatment (number of discharges), as well as the initial concentration of the microorganisms. The data on the most efficient modes of the electropulse treatment of a water medium are presented.