Diffusive boundary layers (DBL), sediment oxygen flux, and natural passive flow through model macrofauna burrows were compared in two benthic chambers: one with a conventional rotational stirrer and the other with a two-dimensional flow diffuser system. Oxygen microprobe profiles showed that at similar velocities the mean diffusive boundary layer (DBL) thickness induced by a conventional rotor stirrer (453 ± 118 µm) was not significantly different to that produced by the diffuser system (403 ± 53 µm). The rotor produced twice as much DBL spatial variability (coefficient of variation 27%) as the diffuser (CV 11%). Variability between the rotor system’s DBL transect replicates was also two times greater (average CV of 22%) compared to the diffuser (CV 14%). At equivalent stirring speeds over experimental sediments, mean O2 consumption rates were also not significantly different between the two systems. The diffuser induced consistently greater (16–37%) passive Bernoullian flow through model macrofauna burrows irrespective of the position of inhalant-exhalent openings. The rotor stimulated anomalous burrow flow regimes over a greater area of the chamber floor (36%) compared to the diffuser (23%). Depending on vent orientation the rotor was shown to reverse (exhalent to inhalant) burrow flow regimes in the central 9% of the chamber floor. This artifact of radial pressure and velocity differentials may have severe implications for tube dwelling infauna that rely on unidirectional flow. The diffuser system more closely mimicked natural two-dimensional water flow over the sediment surface and structures therein and is likely to give more representative results when measuring benthic processes within incubation devices.