We present here a model which couples the hydrologic component and the transport of herbicides within a catchment. The model used takes into account the age structure of the stream water in order to characterize short and long term fluctuations of herbicide flux concentrations. The highly dynamic behavior of herbicides concentrations may lead to the exceedance of specific toxic threshold and is therefore key to exposure risk assessment of aquatic ecosystems. The model is based on a travel time formulation of transport embedding a source zone that describes near surface dynamics. Travel time distributions are analytically derived for the case of solutes subject to partial intake from vegetation and chemical degradation. The framework developed is evaluated by comparing modeled hydrographs and atrazine chemographs with those measured in the Aabach agricultural catchment (Switzerland). The model proves reliable at representing the specific transport features shaped by the interplay of long term processes (persistence of solute compounds in soils), short and long term hydrological transport related to the temporal structure of rainfall. It also allows evaluating the effects of the stochasticity of rainfall patterns and application dates on the export dynamics of herbicides. This exercise is further confronted to recent data obtained during three spring storm events in a tributary of Lac Léman. Nineteen herbicide compounds were analyzed at four sampling stations dispatched along the stream network. The occurrence of the substances, their specific release dynamics during storms are further discussed in regards to the atrazine data in the Aabach catchment and the model capability.