Microzooplankton (microZP, protists) and mesozooplankton (mesoZP, metazoans) abundances and biomass as well as presence of domoic acid (DA, phycotoxin) during the mesocosm experiment in the Canary Islands in autumn 2019. Depth-integrated (0-2.5m) water samples were taken over the course of 33 days, in 2-day intervals for microZP and mesoZP and 4-day intervals for DA. MicroZP was assessed by Utermöhl light microscopy and its biomass estimated using biovolume to carbon conversion factors from the literature. MesoZP samples were split into three size fractions (55-200, 200-500 and >500 µm), preserved with 70% ethanol and assessed under a stereo microscope. For biomass, mesoZP were measured in an element analyser. MesoZP data is provided for copepods only (dominant group) and all metazoan zooplankton combined (mainly copepods and appendicularians). For DA, particulate matter was filtered (>0.7µm) and analysed via liquid chromatography and tandem mass spectrometry. The upwelling treatment started on day 6. Methodological details in Goldenberg et al. (doi:10.3389/fmars.2022.1015188) and Goldenberg et al. (under review).