Abiotic parameters such as light, temperature, nutrient availability and inorganic carbon source are known to vary widely between immersion and emersion. We measured gross community productivity (GCP) and community respiration (CR) over spring tidal cycles in intertidal Zostera marina and Z. noltii communities. CO2 fluxes during emersion and inorganic carbon fluxes during immersion were assessed using closed benthic chambers. GCP and CR rates were significantly higher during immersion than during emersion for both communities. In July, GCP rates were 3- and 5-fold higher and CR rates were 2.5- and 9-fold higher during immersion for the Z. marina and Z. noltii communities, respectively. This trend was confirmed in the Z. noltii community at different periods of the year (February, April and November). Neither photoinhibition nor desiccation was measured during emersion, but shading might have greatly limited the GCP rates. Higher CR during immersion could be explained by enhanced bacterial and infaunal activity.