Occurrence and concentration of a broad spectrum of micropollutants are investigated in Austrian river catchments, namely polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs), organotin compounds, perfluoroalkyl acids (PFAAs) and metals. The parallel analysis across multiple environmental and engineered compartments sheds light on the ratio of dissolved and particulate transport and on differences in concentration levels between point and diffuse emission pathways. It is found that some PAHs and organotins are present in rivers, groundwater and bulk deposition at higher concentrations than in municipal wastewater effluents. Among PFAAs and metals, highest concentrations were recorded either in atmospheric deposition or in discharges from wastewater treatment plants. The relevance of the analysis across compartments is best shown by the case of perfluorooctanesulfonic acid (PFOS). Despite municipal wastewater effluents being the emission pathway with highest concentrations, this study reveals that not only rivers, but also atmospheric deposition and groundwater sometimes exceed the environmental quality standard for surface waters. Moreover, this work reveals partially counterintuitive patterns. In rivers with treated wastewater discharges, increasing levels of dissolved compounds were measured at rising flow conditions, whereas the opposite would be expected owing to the dilution effect. This might derive from the mobilisation from soil or suspended particulate matter or rather find its explanation in high concentrations in atmospheric deposition. These hypotheses require however being tested through targeted studies. Additional future research includes the analysis of how regional or catchment specific characteristics might alter the relative importance of different emission pathways, and the modelling of emission and river loads to assess their relative contribution to river pollution.