Rising pesticide levels in streams draining intensively managed agricultural land have a detrimental effect on aquatic ecosystems and render water unfit for human consumption. The Soil and Water Assessment Tool (SWAT) was applied to simulate daily pesticide transfer at the outlet from an agriculturally intensive catchment of 1110 km(2) (Save river, south-western France). SWAT reliably simulated both dissolved and sorbed metolachlor and trifluralin loads and concentrations at the catchment outlet from 1998 to 2009. On average, 17 kg of metolachlor and 1 kg of trifluralin were exported at outlet each year, with annual rainfall variations considered. Surface runoff was identified as the preferred pathway for pesticide transfer, related to the good correlation between suspended sediment exportation and pesticide, in both soluble and sorbed phases. Pesticide exportation rates at catchment outlet were less than 0.1% of the applied amount. At outlet, SWAT hindcasted that (i) 61% of metolachlor and 52% of trifluralin were exported during high flows and (ii) metolachlor and trifluralin concentrations exceeded European drinking water standards of 0.1 μg L(-1) for individual pesticides during 149 (3.6%) and 17 (0.4%) days of the 1998-2009 period respectively. SWAT was shown to be a promising tool for assessing large catchment river network pesticide contamination in the event of floods but further useful developments of pesticide transfers and partition coefficient processes would need to be investigated.