The ingestion rates of three Acartia tonsa life-stages (N4-nauplii, C4-copepodites and adult copepods) feeding on three different strains of A. pseudogonyaulax, isolated from the Danish Limfjord, were determined by means of bottle incubation experiments. In the same experiment the intracellular goniodomin A (GDA) content of A. pseudogonyaulax was determined by LC/MS-MS analysis. In addition, the adverse effects of A. pseudogonyaulax culture supernatants on the hatching rate success of A. tonsa and the metabolization/excretion rate of GDA by A. tonsa were assessed. This dataset contains all data collected within these experiments including cell counts, GDA toxin contents and particular organic carbon and nitrogen contents of A. pseudogonyaulax. The preparation and execution of the experiments were carried out between May 1 and July 15, 2022 in the laboratories of the Alfred-Wegener-Institute, Helgoland, Germany.