The simulation of the impact of Escherichia coli loads from watersheds is of great interest for assessing estuarine water quality, especially in areas with shellfish aquaculture or bathing activities. For this purpose, this study investigates a model association based on the Soil and Water Assessment Tool (SWAT) coupled with a hydrodynamic model (MARS 2D; IFREMER). Application was performed on the catchment and estuary of Daoulas area (France). The daily E. coli fluxes simulated by SWAT are taken as an input in the MARS 2D model to calculate E. coli concentrations in estuarine water and shellfish. Model validation is based on comparison of frequencies: a strong relationship was found between calculated and measured E. coli concentrations for river quality (r2 = 0.99) and shellfish quality (r2 = 0.89). The important influence of agricultural practices and rainfall events on the rapid and large fluctuations in E. coli fluxes from the watershed (reaching three orders of magnitude in <24 hours) is one main result of the study. Response time in terms of seawater quality degradation ranges from one to two days after any important rainfall event (greater than 10 mm⁄ day) and the time for estuary to recover good water quality also mainly depends on the duration of the rainfall. In the estuary, three effects (rainfall, tidal dilution, and manure spreading) have been identified as important influences.