Description: The data were generated during an experiment simulating different frequencies of heatwaves (zero, one and three) in late spring/summer 2015. The experiment was carried out at the Kiel Outdoor Benthocosm (KOB) of GEOMAR Helmholtz Centre for Ocean Research Kiel, located at the Kiel Fjord. The biomass of filamentous algae was quantified from the most abundant genus occurring inside the tanks, i.e. Ceramium sp. The biomass of Zostera marina and Fucus vesiculosus was estimated from growth rates measurements carried out every 15 days. The biomass of all macrophytes was converted to carbon using specific carbon contents measured concomitantly with stable isotopes (https://doi.pangaea.de/10.1594/PANGAEA.966179). Respiration and primary production measurements were carried out on 09.08.2015 for filamentous algae, and on 12.08.2015 for Fucus vesiculosus. To execute these measurements, organisms were kept in gas-tight cylindrical chambers equipped with sensor spots for non-invasive oxygen measurements, which allowed continuous oxygen logging. Throughout the measurements, the chambers were kept inside the KOB tanks to maintain the temperature. The oxygen values were converted to carbon and normalized by the area of the tank (1.53 m2) per day. Note that the data of net primary production and respiration rates of the Z. marina were previously published (https://doi.org/10.1594/PANGAEA.904632). The carbon flux refers to the exports, i.e. biomass that was floating in the tanks, which was considered as carbon leaving (i.e. exported outside of) the system but still usable. The material to quantify the exports was collected every seven days, separated accounting for the contribution of each macrophyte group, dried at 80 °C until the biomass was constant and weighted. The dry weight was converted to carbon using the specific carbon contents measured concomitantly with stable isotopes (https://doi.pangaea.de/10.1594/PANGAEA.966179), and normalized by the area of the tank (1.53 m2) per day.