Rainfall and river flows are environmental variables influencing the microbial status of bivalve mollusc harvesting areas. This study investigated spatial and temporal relationships between rainfall, river flows and concentrations of Escherichia coli in mussels (Mytilus spp.) and Pacific oysters (C. gigas) from three harvesting areas in the Dart Estuary over the period 1996–2009. Mussels growing on the riverbed were found to be more contaminated than oysters growing in the water column. A step change in the levels of the microbial indicator was identified in both species from all harvesting areas. The highest levels of E. coli were detected when total rainfall exceeded 2 mm and water levels in the main tributaries exceeded the mean flow. The magnitude of response in levels of E. coli to these hydrological events varied between species and monitoring points, but was consistently higher between the 3rd and 4th days after the rainfall event. This lag time is assumed to result from catchment topography and geology determining peak levels of runoff at the headwaters 12–24 h after rainfall events. It is considered that future risk management measures may include sampling targeting hydrograph events.