The extent of Zostera spp. meadows in Arcachon Bay has drastically decreased in the last 20 years and a significant increase of suspended sediment concentration was observed in the meantime. Zostera spp. are well known ecosystem engineers able to reduce near-bed currents and promote sediment accretion; it is then suggested that such decline may lead to the observed increase of sediment re-suspension. Main consequences are an increase of net erosion trends on tidal flats, and a decrease of light penetration in the water column. In this context, this study focuses on spatio-temporal analysis of seagrass decline in relation with morphological and hydrodynamical changes in the Bay. Historical bathymetric charts and maps of Zostera beds extent were co-analysed. In addition, MARS3D, a numerical model that explicitly takes into account the damping effect of Zostera on flow velocity was used to simulate depth-averaged and near-bed velocity fields for the various configurations derived from the available historical data. Results firstly highlight that both Zostera noltei and Zostera marina principally declined in the deeper parts of the bay as well as in the inner parts of the bay, suggesting that the observed increase of suspended sediment concentration may have contributed to the regression of both species. Moreover, Z. noltei also significantly regressed close to channel edges and mostly where Z. marina disappeared. The simulations show that near-bed velocities increased in the channel edges where Z. marina disappeared. It can also be safely expected that Z. marina decline has promoted erosion on channel edges inducing both decrease of light penetration and mechanical wrenching of neighbourhood Z. noltei. Regression of Z. noltei also significantly impacts both near-bed and the global tidal circulation within the Bay. This study tends to confirm the hypothesized feedback loop between Zostera decline and hydro- and sediment dynamics.