The data refer to 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 organisms were collected from the mesocosm tanks, stored at -80 °C, dried at 60 °C for at least 48 hours, and ground with agate mortar and pestle. The ground material was subsampled, weighed and placed into tin capsules (3.2 × 4.0 mm, Hekatech, Wegberg, Germany). These samples were analysed with an elemental analyser system (NA 1110, Thermo, Milan, Italy) connected to a temperature-controlled gas chromatography oven (SRI 9300, SRI Instruments, Torrance, CA, USA) and to an isotope-ratio mass spectrometer (DeltaPlus Advantage, Thermo Fisher Scientific) as described in Hansen et al. (2009), https://doi.org/10.1002/rcm.4267.