This study aimed to investigate the impact of small tributaries on seawater and shellfish quality in coastal area subjected to brief episodes leading to fecal contamination. Escherichia coli and F-RNA-specific bacteriophages were selected as fecal indicators and astroviruses were chosen as being representative of pathogens in the human population during winter viral epidemics. A two-dimensional hydrodynamic model was built to simulate the current and dispersion in the model domain, which includes areas uncovered at low tide. The model also includes decay rates to simulate microorganism behavior and assess the influence of fecal input on shellfish quality. The originality lies in the fact that specific features of the study area were considered. Modeling results indicate limited particle movements and long flushing times at the back of the bay, where shellfish are farmed. Computational results showed that under normal conditions, i.e. 94% of the time, when rainfall was less than 10 mm per day, the sector shows acceptable water quality. These results are in agreement with shellfish concentration measured in the field. Under high flow conditions, high concentrations of fecal indicators and astrovirus were measured in the river and tributaries. The corresponding fluxes were over 50 times higher than under normal weather conditions. The location of the shellfish beds near the coast makes them vulnerable and fecal indicators and viruses were detected in shellfish after short rainfall events. Our modeling approach makes a contribution to shellfish management and consumer protection, by indicating the "risk period" as defined by EU regulations. Molecular development such as viral quantification in conjunction with model developments will help to prevent shellfish contamination and thus provide safer products to consumers and an effective tool for shellfish producers.