The concentration profile of 40 polyfluoroalkyl substances (PFAS) in surface water along the River Rhine watershed from the Lake Constance to the North Sea was investigated. The aim of the study was to investigate the influence of point as well as diffuse sources, to estimate fluxes of PFAS into the North Sea and to identify replacement compounds of perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA). In addition, an interlaboratory comparison of the method performance was conducted. The PFAS pattern was dominated by perfluorobutane sulfonate (PFBS) and perfluorobutanoic acid (PFBA) with concentrations up to 181 ng/L and 335 ng/L, respectively, which originated from industrial point sources. Fluxes of SigmaPFAS were estimated to be approximately 6 tonnes/year which is much higher than previous estimations. Both, the River Rhine and the River Scheldt, seem to act as important sources of PFAS into the North Sea.