Due to new usages and sources, copper (Cu) concentrations are increasing in the Arcachon Basin, an important shellfish production area in France. In the present paper, the trophic transfer of Cu was studied between a microalga, Tetraselmis suecica, and Crassostrea gigas (Pacific oyster) spat. An experimental approach was developed to assess Cu exposure, transfer and toxicity on both phytoplankton and spat. Exposure of microalgal cultures to Cu for 7–8 days (3.1 ± 0.1, 15.7 ± 0.2 and 50.4 ± 1.0 μg Cu·L−1 for the control, Cu15 and Cu50 conditions, respectively) led to concentrations in microalgae (28.3 ± 0.9 and 110.7 ± 11.9 mg Cu·kg dry weight−1 for Cu15 and Cu50, respectively) close to those measured in the field. Despite Cu accumulation, the physiology of the microalgae remained poorly affected. Exposed cultures could only be discriminated from controls by a higher relative content in intracellular reactive oxygen species, and a lower relative content in lipids together with a reduced metabolic activity. By contrast, the fatty acid profile of microalgae was modified, with a particularly relevant lower content of the essential polyunsaturated fatty acid 22:6n-3 (docosahexaenoic acid [DHA]). Following 21 days of spat feeding with Cu15 and Cu50 microalgal cultures, trophic transfer of Cu was observed with a high initial Cu concentration in spat tissues. No effect was observed on oxidative stress endpoints. Cu exposure was responsible for a decrease in the spat condition index, an outcome that could be related to an insufficient DHA supply and extra energy demand as suggested by the overexpression of genes involved in energy metabolism, ATP synthesis and glycogen catabolism.