Sediment-water fluxes of hydrophobic organic chemicals (HOC) may affect the quality of surface waters. Here, we present an approach to derive such fluxes from (a) in situ HOC concentration gradients measured with passive samplers and (b) mass transfer coefficients measured with a novel flux method using Empore disks. For eight undisturbed sediments, this method identified whether the sediment acted as a source or as a sink for HOCs. The analysis also identified which type of transport resistance governed sediment water exchange. For seven inland locations, exchange was limited by benthic boundary layer transport, showing no dependencies on sediment or chemical properties other than concentration. For one river mouth location, exchange was limited by slow in-bed intraparticle diffusion. A biphasic dual compartment radial diffusion model adequately described the data for this location. Fast desorption was interpreted as molecular diffusion retarded by microscale dual domain sorption to amorphous as well as black carbon (BC). Slow desorption was invariant with LogK(ow) and consistent with intraorganic matter diffusion through BC particles. Finally, it is discussed how these findings can be translated into a general framework for flux based exposure assessment.