The Gironde Estuary, one of the largest European ones, presents temporary low dissolved oxygen content in its fluvial section close to the Bordeaux urban area. In a context of population growth and of long-term environmental changes, the development of a high-frequency monitoring programme of the fluvial-estuarine system of the Gironde, called MAGEST (MArel Gironde ESTuary), had appeared essential to address current and future water-quality issues/evaluations. The objectives of the MAGEST survey program are to establish a reference database to improve the knowledge of the Gironde Estuary functioning, encompassing the aspects of hydrology, sediment dynamics and biogeochemistry. Through examples of results from intratidal to seasonal time scales, we demonstrate how such a long-term, high-frequency monitoring of a fluvio-estuarine system is of valuable interest to extract the main trends of its functioning and of the water quality in relation to external forcings (climatology, urban wastes, land use, ...) and to predict the future evolution of an estuary with global and environmental changes.