Abstract <p>The formation of disinfection byproducts hazardous to human health in the process of treatment with chlorine-containing reagents and ozone and the existing risks of converting microorganisms into a viable, but uncultivable state, in which they are able to sustain high doses of disinfecting reagents, are an essential short coming of traditional disinfection methods. This causes the relevance of studies on the search for innovative water disinfection methods, in particular, with the use of environmentally friendly reagents—carbon dioxide and chitosan. In this study, the possibility of <i>Esсheriсhia&#xa0;coli</i> (<i>E.&#xa0;coli</i>) inactivation in real natural water of hydrocarbonate type with low-pressure (0.2-MPa) is estimated for the first time. It has been revealed that the efficiency of disinfection from <i>E.&#xa0;coli</i> in natural water is much lower than in distilled water under the same treatment conditions. It has been established that the efficiency of disinfection with low-pressure СО₂ also essentially decreases in model solutions, which contain bicarbonate, chloride, or sulfate ions. It has been shown for the first time that the action of СО₂ (0.2 MPa) together with chitosan (1 mg/dm³) has a synergetic effect of <i>E.&#xa0;coli</i> inactivation in natural water and provides a high degree of its disinfection from this sanitary-significant microorganism.</p>