Photosystem II (PSII) herbicides have been shown to affect the photosynthesis of corals at low, environmentally relevant concentrations. The recent detection of the PSII herbicide Irgarol-1051 in coastal waters of Hong Kong at concentrations above the EC(50) for reduction of photosynthesis of corals prompted further investigation into the extent of PSII herbicide pollution in coral reefs of Hong Kong. Snap-shot and passive samples were taken from coral reef sites and evaluated via HPLC/MS-MS and a novel bioanalytical technique. Low concentrations (less than 10 ng L(-1)) of diuron and atrazine were found at all study sites. Extracts from these samples concentrated by a factor of 10 were found to reduce the photosynthetic yield of zooxanthellae. It appears unlikely that herbicide pollution is a key issue in isolation but may act synergistically with other stressors to reduce the viability of Hong Kong's coral reefs. The study has also demonstrated the feasibility of combining sample extraction techniques with a coral specific bioanalytical technique for a sensitive assessment of risks associated with herbicide exposure in corals.