Benthic oxygen profiles were acquired using microsensors over two seasonal cycles (December 2001, April and August 2002, January and May 2003) at two stations differently affected by shellfish farming activity in the Thau lagoon (French Mediterranean coast). This study was part of the Microbent-PNEC Program on the study of biogeochemical processes at the sediment–water interface in an eutrophicated environment. We explored seasonal and spatial heterogeneity as well as the biogeochemical drivers of oxygen uptake, such as in situ temperature, bottom water oxygenation and organic matter deposition. O2 consumption rates were determined by using a transport-reaction model. Maximum rates were reached in August and May and minimum rates in December, April or January. The effect of oyster farming on oxygen fluxes was clearly identified with higher diffusive oxygen uptake in the station inside the oyster parks (C5; 36.8 ± 18.5–87.7 ± 40.8 mmol m−2 d−1), compared with the station lying outside the oyster parks (C4; 8.6 ± 2.1–30.7 ± 8.3 mmol m−2 d−1). At C5, the large spatial heterogeneity was statistically concealing temporal variation, whereas a clear statistical difference between cold and warm periods appeared at C4. In these lagoon sediments, the seasonal dynamics of diffusive oxygen demand and consumption rates were mainly driven by seasonal temperature variation at both stations, as well as by seasonal organic matter delivery to the sediment at the station located outside the oyster parks. In the station located below the oyster parks, seasonal variation of organic matter deposition was dampened by oyster filtering activity. Seasonal temperature variation thus appeared as the major driver of oxygen dynamics in this station. Measurements of total O2 uptake rates indicated a significant fraction of microbial recycling and diffusive transport in oxygen uptake at the station located close to the oyster parks. In the open water site, fauna-mediated O2 transport prevailed in April 2002 (cold conditions), whereas the microbial recycling seemed to dominate in May 2003 (warm conditions).