This dataset contains species-resolved phytoplankton and microzooplankton abundance and biomass data from the KOSMOS 2023 Helgoland mesocosm experiment conducted in the coastal waters off Helgoland Island in the North Sea, Germany. The experiment investigated the effects of Ocean Alkalinity Enhancement (OAE) on plankton communities during the development of a natural spring bloom. Six mesocosms (~6 m³) were subjected to an immediate dilution OAE scenario, establishing an alkalinity enhancement gradient ranging from ΔTA 0 to 1250 µmol kg⁻¹ in increments of 250 µmol kg⁻¹ through calcium-based alkalinity addition. The dataset includes taxonomically resolved phytoplankton and microzooplankton abundance (cells mL⁻¹), carbon biomass (µg C L⁻¹), functional group classifications, and World Register of Marine Species (WoRMS) taxonomic identifiers. Associated carbonate chemistry measurements, including total alkalinity (TA), dissolved inorganic carbon (DIC), pH, fugacity of carbon dioxide (fCO₂), salinity, temperature, and calculated ΔTA values are provided for each sampling event.