Mesozooplankton trophic markers to estimate food web length (δ15N) and dietary contribution of diatoms (fatty acids) during the mesocosm experiment in the Canary Islands in autumn 2018. Depth-integrated (0-14 m) plankton nets were taken and omnivorous copepods >200µm used for trophic marker analysis. For trophic level, copepods were picked in groups into tin capsules and δ15N measured in a mass spectrometer. Particulate organic matter (>0.7µm) δ15N was also measured to calculate an autotroph baseline. The difference between copepod and autotroph δ15N was used as trophic level proxy. Trophic level data represents averages across all samples from day 11 to 38. For fatty acids (FA), copepods were picked in groups and FA composition determined by gas chromatography. Particulate organic matter (>0.7µm) FA were also measured as baseline. The marker 20:5ω3/22:6ω3 was most suitable to track the propagation of diatom productivity up the food web. FA data represents averages across samples taken on day 30 and 36. The upwelling treatment started on day 4. Methodological details in Ortiz et al. (2022) (doi:10.3389/fmars.2021.743105), Baumann et al. (2021) (doi:10.3389/fmars.2021.742142) and Goldenberg et al. (under review).