Seagrasses are important habitat-formers and facilitator species that form the basis of complex ecosystems in estuaries throughout the world. However, general worldwide declines in seagrass beds have been reported with (invading) bloom-forming seaweeds, which threaten to displace the seagrasses and change the ecosystem fundamentally. We compared the functioning of the community with the intertidal seagrass Nanozostera noltii as the only macrophyte, in a mixed status with the invasive drift seaweed Gracilaria vermiculophylla and with only G. vermiculophylla as macrophyte. These assemblages represent different phases of seaweed invasion. Assemblage functioning was assessed as the metabolic state of the system based on carbon dioxide and oxygen metabolism during submerged and emerged conditions. Across all assemblages production rates were much higher during submerged than during emerged conditions. Assemblage productivity increased from monospecific N. noltii, through mixed to monospecific assemblages of G. vermiculophylla. However, the photosynthetic efficiency at low light intensities (α) of N. noltii assemblages was higher than those dominated by G. vermiculophylla. Metabolic performance patterns were mainly caused by increasing macrophyte biomass from N. noltii to G. vermiculophylla dominated assemblages. Therefore, with the shift from N. noltii to G. vermiculophylla domination, it is likely that these communities will become less efficient, but their productivity will increase considerably.