<p>Water fluxes out of permeable seabeds contribute considerably to the delivery of dissolved matter across the land-ocean pathway. Apart from assessing the net fluxes across the seabed interface, it is important to understand the transport and mixing dynamics to identify where nutrients distribute and accumulate. In shallow and intermediate water depths, the interplay of seabed topography with waves defines the flow in the lower water column. Furthermore, this interaction can induce patterns of advective flow through the seabed, a process known as porewater exchange, which enhances the fluxes across the seabed interface. To advance current knowledge regarding both aspects – net fluxes and the dynamics in the water column – the present study investigates waves interacting with microtopographies of different types, including flat, gravelly, and rippled sandy beds, in a laboratory wave tank setup. A tracer fluid discharges from the seabeds, with its concentration measured simultaneously with the velocity field above them. The results reveal that turbulence, dominating the transport within the water column, increases with the seabed topography size. Regarding the net flux of tracer being affected by porewater exchange, the relation to seabed topography revealed more complexity with wave pumping and flow-topography contributing at varying degrees above the different beds. This produced no consistent order of which seabed induces the highest fluxes across all wave scenarios. With fluxes differing more than twofold between seabeds within each wave scenario, the results underscore the impact of seabed topography. Furthermore, mixing lengths are derived from the experimental data to parametrize water column dynamics.</p>