A study coupling core incubation and a large number of in situ microelectrode measurements (n=18) was performed at a single station in the Golfe de Fos, a semi-enclosed estuarine system in the South of France on the Mediterranean Sea. Total and diffusive oxygen fluxes were determined for two different seasons (October 2000 and May 2001). The average total and diffusive oxygen fluxes were 21.5 and 12.7 mmol m−2 day−1, respectively, in October and 18.5 and 16.5 mmol m−2 day−1, respectively, in May. The average total oxygen demand does not vary significantly between the two periods (21.5±5 to 18.5±4 mmol m−2 day−1). The spread of the values obtained by microelectrode measurements reveals the variability at the decimeter scale indicating a control by small-scale processes. Little difference was found in May between the total and diffusive oxygen fluxes when the number of microelectrode profiles (n=18) and core incubation (n=9) was sufficient to catch larger fluxes linked to “organic hot spots”. Although present at a population density of 5700 individuals for 0.1 m2, macrofauna is mostly composed of surface deposit feeders. The little difference found between total and diffusive oxygen demand points towards not only the population density but also the faunal assemblage as a determining factor for sediment irrigation.