In situ phytoplankton microcosms were developed and characterized for use in toxicity testing. The microcosms contained 225 μm filtered seawater maintained in 1 liter glass bottles attached to a plastic frame and immersed at 3 m under the sea surface. Synechococcus and picoeukaryote population dynamics in microcosms and the surrounding water were compared. A bloom-like behaviour observed for Synechococcus in these phytoplankton microcosms was avoided when 10% of the culture volume was replaced, every two days, by filtered seawater. After 2 weeks, no significant difference in Synechococcus and picoeukaryotes cell counts was observed in microcosms compared to the surrounding free seawater. Synechococcus fluorescence at 545 nm (phycoerythrobilin) fluctuated with a similar pattern in such microcosms and in free seawater and were shown to be correlated to light intensity fluctuations over a two week experiment. The in situ microcosms were used to study the impact of low copper additions. Synechococcus populations were dramatically decreased by copper addition, while picoeukaryote populations were increased simultaneously. Our data show that drastic changes in species composition can occur at copper concentrations encountered in polluted coastal areas.