Coastal bays and estuaries with aquaculture activity may show spatial variability on the exposure at river-borne substances such as nutrients, pesticides or pollutants. In function of the relative geographical position of the rafts and the meteo-oceanographic conditions, the rafts affection from freshwater plume may entail substantial differences. This work evaluates the river-borne affection substances in function of the acute and chronic perspectives. We based on the results of a set of a conservative tracer numerical experiment designed to cover a wide range of meteo-oceanographic conditions. The indexes are obtained for a shallow and micro-tidal bay (i.e. Fangar Bay) where the 3-D TELEMAC numerical model is implemented. The numerical model in Fangar Bay is calibrated and verified using “in situ” current meter data, lagrangian buoys and CTD profiles. The exposure assessment helps to understand the spatial-temporal variability of the dynamics within the bay and the conclusions may support the developing of sustainable aquaculture activities.