Background: Understanding the effects of anthropogenically-driven changes in global temperature, atmospheric carbon dioxide and biodiversity on the functionality of marine ecosystems is crucial for predicting and managing the associated impacts. Coastal ecosystems are important sources of carbon (primary production) to shelf waters and play a vital role in global nutrient cycling. These systems are especially vulnerable to the effects of human activities and will be the first areas impacted by rising sea levels. Within these coastal ecosystems, microalgal assemblages (microphytobenthos: MPB) are vital for autochthonous carbon fixation. The level of in situ production by MPB mediates the net carbon cycling of transitional ecosystems between net heterotrophic or autotrophic metabolism. In this study, we examine the interactive effects of elevated atmospheric CO concentrations (370, 600, and 1000 ppmv), temperature (6°C, 12°C, and 18°C) and invertebrate biodiversity on MPB biomass in experimental systems. We assembled communities of three common grazing invertebrates (Hydrobia ulvae, Corophium volutator and Hediste diversicolor) in monoculture and in all possible multispecies combinations. This experimental design specifically addresses interactions between the selected climate change variables and any ecological consequences caused by changes in species composition or richness.Results: The effects of elevated CO concentration, temperature and invertebrate diversity were not additive, rather they interacted to determine MPB biomass, and overall this effect was negative. Diversity effects were underpinned by strong species composition effects, illustrating the importance of individual species identity.Conclusions: Overall, our findings suggest that in natural systems, the complex interactions between changing environmental conditions and any associated changes in invertebrate assemblage structure are likely to reduce MPB biomass. Furthermore, these effects would be sufficient to affect the net metabolic balance of the coastal ecosystem, with important implications for system ecology and sustainable exploitation.