Introduction: The epidemic situation in the territory of the Russian Federation is noted for an increase in waterborne diseases and registration of up to 70 % of cases of acute intestinal infections of unknown etiology on certain territories. Numerous cases of gastrointestinal diseases of bacterial and viral etiology associated with the use of water that complies with regulatory requirements validate the importance of improving criteria for pathogen control in water bodies. Objective: To substantiate the expediency to expand the list of key microbiological indicators and standards for an objective assessment of safety of various water bodies. Material and methods: We summarized the results of microbiological testing of water quality and safety in water bodies (potable water, reservoirs, waste water) and substantiated water safety standards proposed by research institutes and centers for hygiene and epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor) for 2010–2020. Sanitary and microbiological indicators of potable water and water bodies in places of water use of the population were analyzed based on data of Annual Report Form No. 18 for 2017–2021. Results: Introduction of new indicators and standards for all coliform bacteria, Escherichia coli, and enterococci to control water safety will ensure the absence of waterborne pathogenic and potentially pathogenic bacteria causing gastrointestinal infections. Noncompliance with regulatory requirements for Escherichia coli and enterococci is a strong evidence of recent fecal pollution and the potential epidemic danger of the aquatic environment. Introduction of the Legionella pneumophila indicator to control safety of hot water of centralized water supply, swimming pools and water parks is aimed at preventing Legionella infections in the population. Discussion: Harmonization of key indicators for all types of water enables determination of the epidemiological significance of a particular water body in transmission of pathogens of intestinal infectious diseases and prediction of the epidemic situation. Conclusions: The adequacy of the detected key indicators of water safety determines health outcomes. Their excess indicates the extent of contamination and related risks for population health and necessitates prompt managerial decisions and appropriate preventive measures to eliminate adverse health effects of microbiological agents.