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Despite 20 years of control on eutrophication, episodes of summer hypoxia still occur in the Loire estuary, impacting water quality and posing a key scientific and management challenge. This work aimed to quantify the contribution of the benthic compartment to hypoxia in the Loire estuary by direct measurement of water–sediment fluxes and an in-depth understanding of the seasonal variations of oxides and phosphorus stocks. During the summer’s low-discharge period, results show that the iron oxide-rich deposit is stable under hypoxic conditions, limiting the release of dissolved phosphorus into the overlying water column. The high nitrate content of the water column appears to be an important oxidizer of iron during hypoxic periods, limiting dissolved phosphorus leakage and aggravation of hypoxia. During the exceptional winter flood, significant sediment erosion associated with bubbling phenomena (attributed to methane efflux) created severe fractures in the sediment and stimulated water–sediment exchange. During the following months, these fractures were progressively filled, which decreased the intensity of benthic fluxes. However, due to the high residence time in the water during the summer period, a simple model demonstrated that benthic contributions were sufficient to directly (by direct oxygen consumption) or indirectly (by promoting ammonia oxidation) affect the oxygen stock in the water column during the low-discharge period. Our study demonstrates the importance of the benthic compartment in the occurrence of hypoxia and the obvious lack of knowledge to illustrate and model the biogeochemical functioning of the estuary.

Although not systematically considered as oxygen minimum zones, River-dominated Ocean Margins are sensitive to oxygen depletions. For example, the continental shelf off the Gironde, which flows into the Bay of Biscay, had not yet been studied from this perspective although recent simulations suggested that this area should already have experienced deoxygenations in recent decades. To fill this gap, profiles of temperature, salinity and dissolved oxygen were performed in the water column of the continental shelf off the Gironde during seven cruises distributed over the different seasons between 2016 and 2021. Turbidity, chlorophyll-a and pH were also measured during some of these cruises. In winter, the water column was slightly stratified due to high river flows. Then, a seasonal thermal stratification was present from spring to autumn. Similarly, dissolved oxygen showed a seasonal dynamic with: a well-oxygenated water column in winter, an oxygen oversaturation in the first 20 meters during the spring bloom, and then a progressive oxygen depletion in bottom waters until reaching an oxygen saturation minimum down to 45% in autumn. These deoxygenations are explained by the seasonal stratification that isolates the bottom waters from spring to autumn, and are likely enhanced by the advection of deoxygenated waters from the north of the Bay of Biscay and the settling of the organic matter produced in surface waters. A better understanding of these processes in the context of global warming undoubtedly requires better documentation of dissolved oxygen variability through the implementation of a long-term and continuous in situ monitoring.