Water quality, in terms of the bacteria and viruses present, affects the incidence of microbial contamination in bivalve molluscs. The European Union Official Control Regulations manage these potential human health risks, requiring all Member States to routinely monitor the level of faecal contamination in production and relaying areas, and to classify these production areas accordingly. How a site is classified can affect business flexibility, operating costs, and even the ability to trade. The protection of public health is the primary remit of the national competent authorities implementing the regulations, while businesses are keen to achieve and maintain a classification indicative of good water quality, and to minimise the likelihood of a site being downgraded or closed. Equally, they do not want to make their customers sick. Balancing protection of public health and the viability of bivalve shellfish production is most easily achieved with a regulatory system that is responsive, adaptive and ultimately risk-based. Despite the standard legislation and supplementary guidance to ensure consistency of approach, interpretation and implementation varies across countries. Some take a risk based and more permissive approach, whilst others are much more restrictive. This indicates the ability of Member States to exert some independence within the overarching legal framework, reflecting regional variation in environmental conditions, historical approaches to shellfish hygiene controls as well as the range of relationships between producers and regulators.