Seagrass meadows modify the flow structure and attenuate current velocities. Over the past decades, seagrasses have drastically declined worldwide, reducing their capacity to regulate flow conditions. Intertidal species have been particularly affected by this decline, yet there is a lack of understanding regarding the influence of intertidal seagrass decline on the hydrodynamics of shallow coastal lagoons. In this study we use a 3D flow-vegetation model that accounts for the full effect of vegetation on mean and turbulent flow, as well as the action of the flow on leaf bending, to study how tidal hydrodynamics respond to the seasonal and multi-decadal changes in intertidal seagrass characteristics at a regional scale. The model is applied to the Arcachon lagoon (France), which is colonized by extensive Zostera meadows (Zostera marina and Zostera noltei). This study reveals that a short-leaf and flexible seagrass species such as Z. noltei can regulate tidal hydrodynamics throughout the lagoon due to the presence of broad and dense meadows on the tidal flats. In summer, seagrass decline leads to a significant increase in flow velocities (+100%) on the tidal flats, but to a decrease in the channels (-20%). However, in winter, the response of tidal hydrodynamics to the reduction in seagrass coverage is far less pronounced. Comparison of various simulated scenarios reveals that the multi-decadal decline of Zostera spp. with summer characteristics and the seasonal loss between summer and winter lead to modifications in tidal flow parameters (current velocities, tidal asymmetry, high tide water level) of comparable intensity.