The World Health Organisation's (WHO) Water Safety Plans highlight the need for preventative risk management when managing water contamination risks. As part of this approach, a management framework incorporating multiple barriers is necessary and there is a need to validate those barriers through scientific evidence. This paper reports on a study undertaken to validate the effectiveness, in terms of pathogen numbers, of having protected watersheds. The study aimed to determine if the deer population in a protected watershed carried Cryptosporidium and whether or not it was human infectious. Deer faecal samples were collected from the protected watersheds over a 12 month period and analysed using a new method, developed as part of this project, for genotyping Cryptosporidium. Early results showed the presence of Cryptosporidium, but following a refinement in the method no human infectious Cryptosporidium was detected. The results give some confidence that having protected watersheds is an effective barrier against pathogen contamination. They do not, however, imply that continued monitoring and management of the deer should cease. To maintain compliance with the Water Safety Plans, continual validation of barrier effectiveness is required.