Intermittent rivers have a specific hydrological behaviour which also influences water quality dynamics. The objective of this work was to model the flow and water quality dynamics of a coastal Mediterranean intermittent river using the Soil and Water Assessment Tool (SWAT 2005). Flow, sediment, nitrogen and phosphorus transport were simulated on the Vene experimental catchment, France. The model was sequentially calibrated at sub-catchment scale and validated both at sub-catchment and catchment scales. A procedure for building the data records for the point sources is presented. The results indicate that, while the model produces good results for flow simulation, its performance for sediment transport is less satisfactory. This in turn impacts on the nutrient transport module. The reasons behind these shortcomings are analysed, taking into account the length of the data records, their distribution and the equations used in the SWAT model. The need for a thorough multi-objective model validation is illustrated.