Abstract Transport and cycling of chemical substances in streaming waters and lakes can be markedly affected by changes in the vertical mixing depth in bed sediments. In mathematical models of the horizontal mass transport coupled to mass retention in bed sediments and biota, reliable parameterizations of the vertical mixing mechanisms are needed. The present study shows how the vertical mixing in bed sediments varies primarily with advective induced diffusion, chemical partitioning (dissolved and particulate phases) and a transport mechanism denoted biotic advection. These mechanisms vary substantially between different aquatic systems and also spatially within a specific system, indicating a variability in active layer thickness. Analytical solutions of the active layer thickness as well as exchange rates are derived for a couple of cases and compared with data of phosphorus transport in agricultural drainage brooks.