Pesticides applied onto agricultural fields are frequently found in adjacent rivers. To what extent and along which pathways they are transported is influenced by intrinsic pesticide properties such as sorption and degradation. In the environment, incomplete degradation of pesticides leads to the formation of transformation products (TPs), which may differ from the parent compounds regarding their intrinsic fate characteristics. Thus, the export processes of TPs in catchments and streams may also be different. In order to test this hypothesis, we extended a distributed hydrological model by the fate and behaviour of pesticides and transformation products and applied it to a small, well-monitored headwater catchment in Switzerland. The successful model evaluation of three pesticides and their TPs at three sampling locations in the catchment enabled us to estimate the quantity of contributing processes for pollutant export. Since all TPs were more mobile than their parent compounds (PCs), they exhibited larger fractions of export via subsurface pathways. However, besides freshly applied pesticides, subsurface export was found to be influenced by residues of former applications. Export along preferential flow pathways was less dependent on substance fate characteristics than soil matrix export, but total soil water flow to tile drains increased more due to preferential flow for stronger sorbing substances. Our results indicate that runoff generation by matrix flow to tile drains gained importance towards the end of the modelling period whereas the contributions from fast surface runoff and preferential flow decreased. Accordingly, TPs were to a large extent exported under different hydrological conditions than their PCs, due to their delayed formation and longer half-lives. Thus, not only their different intrinsic characteristics but also their delayed formation could be responsible for the fact that TPs generally took different pathways than their PCs. We suggest that these results should be considered in risk assessment for the export of agricultural chemicals to adjacent rivers and that models should be extended to include both PCs and TPs.