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This data compilation contains previously published toxicity threshold concentrations of copper, cadmium and zinc on different phytoplankton, as determined by incubation experiments. The data was recalculated to nmol/L for consistency, assuming the following molar masses of copper, cadmium and zinc as 63.546, 112.411 and 65.380 g/mol, respectively, and salinity as 1.025 kg/L. The growth medium is included in the dataset, as well as the environment where the phytoplankton in question may commonly occur (open or coastal ocean).