Surface water pollution with poly- and perfluorinated compounds (PFAS) is a well-recognized problem, but knowledge about contribution of different emission pathways, especially diffuse ones, is very limited. This study investigates the potential of the pathway oriented MoRE model in shedding light on the relevance of different emission pathways on regional scale and in predicting concentrations and loads in unmonitored rivers. Modelling was supported with a tailor-made monitoring programme aimed to fill gaps on PFAS concentration in different environmental compartments. The study area covers the whole Austrian territory including some additional transboundary catchments and it focuses on perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS). These two PFAS are regulated and therefore their production and use in Europe are currently decreasing. Nevertheless, these compounds are still emitted into the environment via legacy pollution and as transformation products from other PFAS. These two compounds were selected for this study in view of the larger information availability compared to other PFAS. Despite considerable uncertainties in the input data, model validations show that this approach performs significantly better than previous modelling frameworks based on population-specific emission factors, population density and wastewater treatment plant information. The study reveals the predominance of emissions via municipal wastewater treatment plants for PFOS and a relevant role of diffuse emission pathways for PFOA. Results suggest that unpaved areas contribute the biggest share to total diffuse emissions, but the estimation of these pathways is affected by the highest uncertainty in the input data and requires better input data from monitoring. Once the currently growing substance-specific data sets on the concentration of PFAS, others than PFOS and PFOA, in different environmental compartments, will reach an adequate quality, the model presented here will be easily applicable to them.