The phycotoxin contents were measured in 2013 during a long-term mesocosm CO2 experiment in Gullmar Fjord (Sweden). The natural plankton community was enclosed in ten pelagic mesocosms and five of the mesocosms were enriched with CO2 to simulate end-of the century ocean acidification while the others served as controls. The data set was used to assess the impact of ocean acidification on harmful algal bloom species and toxins. The Fjord-sample data were taken in close proximity of the mesocosms and were used to assess the phycotoxin contents in the surrounding waters.