Increased CO2 availability to primary producers changes the nutrient stoichiometry of these organisms. As a result, the quality of the primary producers as food for herbivores is affected. Here, we present experimental work showing that the copepod Acartia tonsa feeding on differently grown Rhodomonas salina is indeed affected by the CO2 availability to the algae. We discuss the potential pathways of excreting the carbon that is in excess in high CO2 algae, and consider the possible consequences of different excretory pathways for the ecosystem. Most likely, a continued increase in the CO2 availability for primary production, together with changes in the nutrient loading of coastal ecosystems will cause strong changes in the trophic link between primary producers and herbivores, which in turn will have consequences to higher trophic levels.