In agricultural watershed, pesticide contamination in surface water mostly occurs during flood events. Among all the parameters involved in the contaminations risks, the pesticide application date input was changed within a one-month interval using the Soil and Water Assessment Tool (SWAT) in an agricultural watershed in the South-West of France. The Save River drains an 1110 km² area of essentially wheat, corn, sorghum and sunflower grown with intensive pesticide inputs, mostly herbicides. The SWAT model was applied to simulate daily metolachlor and aclonifen transfer at the watershed outlet from January 2008 to June 2010. Metolachlor is a highly soluble and poorly lipophilic herbicide whereas aclonifen is a poorly soluble and highly lipophilic herbicide. A single watershed average application date established by a 3-year survey (2007-2009) was assumed for each land use. Total metolachlor concentration prediction could be improved by an application timing shift to 3 days later (Daily R² = 0.22 and PBIAS = -57%). Total aclonifen concentration prediction could not be improved by any timing shift in the chosen range of dates. By testing the behaviour of the two molecules, it was shown that sorption processes were driving the transfer. Metolachlor concentration in the channel mostly depended on both discharge and delay between application date and first flood event whereas transfer of aclonifen mostly depended on rainfall intensity for exportation with suspended sediments through surface runoff.