SARS-CoV-2 is mainly transmitted by respiratory droplets and contact with contaminated surfaces. It can be retrieved in faeces but there is no evidence of faecal–oral transmission, which is the main route of contamination in recreational waters. Standard cleaning and disinfecting procedures, microbiological control and health rules aim to prevent infectious risk regardless of the micro-organisms. In the context of progressive lockdown exit and hospital activities recovery, we assessed the risk of SARS-CoV-2 transmission in rehabilitation pools and therapeutic water environments in order to provide specific recommendations to control the spread of SARS-CoV-2 while ensuring essential rehabilitation care for patients.