Routine bacterial monitoring of shellfish beds using indicator species is a common global practice designed to prevent human consumption of contaminated shellfish products. However, current bacteriological monitoring procedures which focus on the quantification of faecal indicator organisms (FIOs) as a proxy for microbial pollution may not be representative of total bacterial contamination levels present in shellfish harvesting areas. The objective of this study was to critically assess the accuracy of current monitoring strategies by quantifying the spatial (lateral and longitudinal distance) and temporal (seasonality and tidal state) concentrations of FIOs (Escherichia coli and total coliforms) within a single intertidal commercially harvested shellfish bed. Spatial and temporal FIO dynamics, including the effects of tidal state and seasonality, were quantified in mussel flesh and sediment samples from a single intertidal mussel (Mytilus edulis) bed. Our results confirmed that FIO concentrations across a shellfish bed were heterogeneous over larger spatial and temporal scales, but showed no relation to the concentrations of autochthonous bacteria, such as Vibrio spp., or the physico-chemical parameters of the sediment. These results have important implications for both public health and the economic prosperity of the shellfish industry, and demonstrate the importance of accommodating both spatial and temporal fluctuations in routine bacteriological monitoring protocols. We conclude that current FIO monitoring procedures may not accurately represent levels of microbial contamination within shellfish harvesting areas and that more robust microbiological testing procedures need developing.