The Gironde Estuary is the largest macrotidal estuary in Western Europa, formed by the Garonne River (where the urban area of Bordeaux is located) and the Dordogne River. One of its main characteristics is the presence of a Turbidity Maximum Zone (TMZ) where heterotrophic processes (organic matter decomposition) are favored and where low penetration of light limits autotrophic processes (photosynthetic activity). Low dissolved oxygen (DO) that could impact aquatic biota occurred exclusively in the fluvial, low salinity and high turbidity sections of the estuary. These environmental concerns have led to study in detail in this work factors that cause estuarine hypoxia. First, I have estimated organic matter and ammonium fluxes from urban inputs in separate and combined sewer network of the Urban Community of Bordeaux, its wastewater treatment plants (WWTP) and combined sewer overflow, to compare them to the upstream watershed inputs. Even if the two WWTPs succeed in significant reduction in organic matter and ammonium contents of effluents, discharges into estuarine waters are important especially during summer, periods while storm events can generate untreated effluent inputs. This work demonstrates the high lability of this urban organic matter through incubation experiments. The dissolved organic carbon and ammonium contents in wastewater consume oxygen. Respirometry experiments allowed us to estimate higher oxygen uptake rates in wastewater than in the waters of the Gironde Estuary. Finally, the analysis of 7-yr data series from the continuous monitoring of the physico-chemical water quality (MAGEST network: MArel Gironde ESTuary) highlights periods of hypoxia in the upstream section of the estuary during pronounced low water around the Bordeaux conurbation. Statistical treatments of the 7-yr time series of DO concentration demonstrate the significant impact of the Bordeaux metropolitan area as it appears that the under-oxygenations increase during marked low water, in the presence of the TMZ, when the water temperature is high, and where the dissolved oxygen content is already low and can be quickly consumed after untreated storm water discharges. This study also shows that the nature of biological treatment used by the WWTPs and the temporary storage capacity of storm water have a critical role in the release of such compounds into the environment. This work finally provides strategies for effluent discharges to water managers, to short and medium terms, based on hydrological and physico-chemical conditions of the environment in order to limit their impact on the water oxygenation of the Garonne River.