In 2020, the 43rd session of the Codex Alimentarius Commission approved the new work entitled “Development of Guidelines for the Safe Use and Reuse of Water in Food Production” proposed by the 51st session of the Codex Committee on Food Hygiene. To support this work, the Joint FAO/WHO Expert Meeting on Microbiological Risk Assessment (JEMRA) was asked to provide scientific advice regarding safe use and reuse of water in the dairy sector. JEMRA convened an online meeting from 14 June to 2 July 2021 to provide clear and practical guidance on risk-based approaches to assess and manage fit-for-purpose water sourcing, use and reuse in the dairy sector. This report describes the output of this meeting to support the decision-making when applying the concept of fit-for-purpose water for use in the production and processing of dairy products.