This paper proposes and tests a model which couples the description of hydrologic flow and transport of herbicides at catchment scales. The model accounts for streamflow components' age to characterize short and long term fluctuations of herbicide flux concentrations in stream waters, whose peaks exceeding a toxic threshold are key to exposure risk of aquatic ecosystems. The model is based on a travel time formulation of transport embedding a source zone that describes near surface herbicide dynamics. To this aim we generalize a recently proposed scheme for the analytical derivation of travel time distributions to the case of solutes that can be partially taken up by transpiration and undergo 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 in defining complex transport features shaped by the interplay of long term processes, related to the persistence of solute components in soils, and short term dynamics related to storm inter-arrivals. The effects of stochasticity in rainfall patterns and application dates on concentrations and loads in runoff are assessed via Monte Carlo simulations, highlighting the crucial role played by the first rainfall event occurring after herbicide application. A probabilistic framework for critical determinants of exposure risk to aquatic communities is defined. Modeling of herbicides circulation at catchment scale thus emerges as essential tools for ecological risk assessment. © 2012 Elsevier Ltd.