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River water cleaning from microorganisms using electrohydraulic discharges and ozonation was investigated. The processed water was highly polluted with the total number of microorganisms (70 400 cfu/mL) and total Escherichia coli bacteria (280 cfu/mL). The processing was conducted in a tube reactor with a hollow needle-rod electrode configuration. A 400-mL sample of river water was treated at different flow rates. Ozonation was performed in a washing bottle with an ozone concentration of 20 g/m3. The corona discharge treatment showed a steady decrease of bacteria and microorganisms but did not kill them completely. Spark discharge killed the bacteria and microorganisms completely; however, its energy efficiency was much lower than that of ozonation. The ozone treatment decreased the concentration of microorganisms and coli bacteria down to 785 and 10 cfu/mL, respectively, in 45 s which resulted in higher energy efficiency than processing using corona and spark discharges. The NPOC analysis of the treated samples showed its concentration of 5 ± 0, 4 ppm in all samples.