The use of roof-collected rainwater as a freely available and sustainable alternative to drinking water produced by drinking water companies increases worldwide. Initially, rainwater is free of microbial contamination, but it may become contaminated by animals and humans or, alternatively, human pathogens may grow in stored rainwater resulting in a significant human health risk from infectious diseases. This three-year study demonstrated that rainwater stored in different reservoirs in The Netherlands was frequently faecally contaminated and incidentally contained potential human pathogens such as Campylobacter, Cryptosporidium, Giardia, Aeromonas hydrophila and Legionella. Analysis of samples during a period with variable weather conditions showed a correlation between rainfall intensity and faecal indicator counts and increased detection of pathogens after heavy rainfall incidents. Outside temperature had a limited effect on both the temperature and the microbiological quality of the water in the reservoirs, which did not comply with Dutch drinking water legislation and should thus not be consumed without treatment. In general, a health risk may arise from exposure to pathogens when contaminated droplets are inhaled, ingested or come into contact with the skin. Health risks may be reduced by regular cleaning of the collection, storage and transport means, but to assess their efficacy field intervention studies are required.