Hydrographic and water quality surveys of the Motueka River and its river plume were conducted during a moderate flood event (peak flow of 420 m3/s) to assess the source and fate of faecal contaminants transported into Tasman Bay. Escherichia coli (E. coli) and enterococci concentrations in the river were up to 10000 and 7300 Most Probable Number (MPN)/100 ml during peak flow, respectively. A coastal survey revealed a shallow low-salinity plume that extended at least 6 km into Tasman Bay and the region's largest aquaculture management areas (AMAs). Mussels within the influence of the river plume, including those collected within an AMA, had E. coli and enterococci concentrations as high as 1300 and 2200 MPN/100 g tissue, respectively. Application of microbial source tracking markers using end-point PCR assays identified the presence of faecal contamination from ruminant animals (cows, sheep) in water and mussel samples. The detection of ruminant faecal contamination within shellfish located 6 km offshore highlights the close connection between land use and the quality of New Zealand's highly valued coastal resources.