Biofilm-based passive aeration systems (PAS) have attracted recent attention as alternative energy efficient and low maintenance technologies for wastewater treatment. However the modelling of biofilm-based PAS offers unique difficulties for engineers and scientists. One such technology is the pumped flow biofilm reactor (PFBR); a batch biofilm technology. The PFBR employs a unique hydraulic regime which, while enabling aerobic, anoxic and anaerobic conditions to be sequenced, poses a particular challenge to modellers. Furthermore, as the technology employs passive aeration the determination of, and modelling of, oxygen transfer rates and the concentration profiles of oxygen within the biofilm can be difficult. This study investigates a novel method of measuring oxygen concentrations at the substratum level (ie the base of the biofilm layer) using a ‘RedEye (TM)’Oxygen Sensor Patch. This could allow for improved descriptions of how oxygen transfers through biofilms and can test this methodology of measuring contaminant diffusion into biofilms using measurements at the substratum level. In parallel bulk fluid dissolved oxygen concentrations are measured. Thus, uniquely, both the bulk fluid and biofilm base dissolved concentrations are passively measured. The results are modelled using GPS-X (Hydromantis Inc.) software and calibrated against experimental data from the laboratory scale PFBR reactor.