In agricultural watersheds, pesticide contamination in surface water mostly occurs during stormflow events. When modelling pesticide fate for risks assessment, the application timing input is one of the main uncertainty sources among all the parameters involved in the river network contaminations process. We therefore aimed to assess the sensitivity of the river network pesticide concentration patterns to application timing shifts within a plausible range of application dates, considering two pre-emergence herbicides (metolachlor and aclonifen) characterised by two different octanol/water partition coefficients (Kow). The Soil and Water Assessment Tool (SWAT) was applied in the 1110 km2 agricultural watershed of the river Save (south-western France), where wheat, maize, sorghum and sunflower are intensively grown. The pesticide application date was changed within a one-month interval and the pesticide concentration at catchment outlet was simulated from March to June 2010. Total metolachlor concentration prediction could be improved by an application timing shift to 3 days later (Daily R2 = 0.22 and PBIAS = − 57%). By testing the behaviour of the two molecules, it was shown that sorption processes were influencing the control of application timing on the transfer to surface water:metolachlor concentration in the channel depended on both discharge and delay between application date and first stormflow event whereas the transfer of aclonifen depended on rainfall intensity for exportation with suspended sediments through surface runoff. At last, the study discusses the potential implications of the sensitivity in terms of regional agricultural management practice design.