Particle supported autotrophic biofilms were cultivated in external-loop airlift reactors at two different pumice concentrations. Oxygen microelectrodes were used to investigate substrate transport and conversion. A special flow cell was designed for the measurement of oxygen concentration profiles in the particle supported biofilms under defined hydrodynamic conditions. The oxygen concentration profiles inside the biofilms were found to be steeper at high flow velocities in the bulk phase of the flow cell compared to those at low flow velocities. Furthermore, the oxygen flux increased and the thickness of the concentration boundary layer decreased with increasing flow velocity. This dependence was found to be more pronounced in less dense biofilms out of airlift reactors with lower pumice concentrations. In addition confocal laser scanning microscopy (CLSM) was used to visualize the biofilm structure. The volume fractions of bacteria and extracellular polymeric substances (lectin-specific EPS-glycoconjugates) were measured in living fully hydrated biofilms. Both the microelectrode and CLSM measurement showed the influence of shear stress on particle supported biofilms. A higher particle concentration led to dense biofilms with a homogeneous surface, lower thickness of the concentration boundary layer and steeper oxygen concentration profiles. The combination of both techniques allows a detailed and quantitative characterisation of particle associated biofilm structure and function.