The Banc d′Arguin is a marine ecosystem of global conservation significance, the largest bird sanctuary of western Africa, supported by one of the most extensive seagrass beds in the world composed by three seagrass species, two temperate near their southern limit (Zostera noltei and Cymodocea nodosa) and one tropical at its northern limit (Halodule wrightii). Here we predict the fate of this seagrass ecosystem under climate change scenarios during the 21st century, using species distribution models and sea level rise estimates. We forecast a probable decline in total seagrass area of 3340 Km2 (78%) by 2100, involving the loss of both temperate seagrasses (Z. noltei, C. nodosa), the foundational ecosystem components. By 2050, only the tropical species (H. wrightii) would remain, which forms thin and sparse shallow stands functionally distinct from the previous tall dense meadows that span wider vertical ranges. Intertidal flats, the essential bird foraging habitats, would become unvegetated and also suffer a major reduction in area (114 km2 by 2050, 587 km2 by 2100). The large projected loss of foundational seagrass species portends a collapse of major ecosystem functions with profound impacts on biodiversity, fishery resources and ecosystem services.