In this study we investigated the effect of artificial upwelling with different Si:N ratios on a natural oligotrophic plankton community. Data on primary production, flow cytometry, photophysiology, internal nutrient storage, diatom size, diatom silicification and diatom carbon density from the mesocosms experiment conducted on the Canary Islands in autumn 2019. Values are depth-integrated averages in (mostly) 2-days intervals over the course of 33 days. The upwelling treatment started on day 6. All samples were depth integrated (0-2.5m). Oxygen production and respiration rates were measured through incubations and Winkler titrations. Flow cytometry and photophysiology samples were measured fresh. Parameters used for diatom per capita size, silicification and carbon density measurements were taken from the following published datasets on the same experiment: https://doi.org/10.1594/PANGAEA.954852 and https://doi.org/10.1594/PANGAEA.951417