Pigment concentration and pigment-based phytoplankton community composition data from the mesocosm experiment conducted in the Canary Islands in autumn 2019. Depth-integrated (0-2.5m) water samples were taken in 2-days intervals over the course of 33 days. One set of filters (one filter per sampling day and mesocosm) was analysed fluorometrically for Chl a. Another set of filters was analysed for a range of photosynthetic pigments using reverse-phase high-performance liquid chromatography (HPLC). Based on pigment concentrations, phytoplankton community composition was approximated using Chemtax v.1.95 with pigment ratios from Higgins et al. (2011, doi: 10.1017/CBO9780511732263.010). The input included Chl a, b, c2, and c3, peridinin, 19'-butanoyloxyfucoxanthin, fucoxanthin, neoxanthin, prasinoxanthin, violaxanthin, 19'-hexanoyloxyfucoxanthin, alloxanthin, and zeaxanthin. Divinyl Chl a was instead fully associated with Prochlorophyceae. The presence of the main phytoplankton groups is expressed in Chl a equivalents and their contribution to the phytoplankton community as percentage to total Chl a. The upwelling treatment started on day 6. Methodological details in Goldenberg et al. (doi:10.3389/fmars.2022.1015188).

The values marked with ? (HPLC day 19 mesocosm 1) must be errornous. Exclude from analysis.