We evaluated the acute toxicities of metals cadmium (Cd), copper (Cu) and nickel (Ni) to a widely-distributed copepod Eurytemora affinis isolated from the Seine estuary. Both sexes of adult E. affinis were exposed separately to the three metals at concentration gradients to determine its 50% lethal concentration (LC50). After 4 days of exposure, both males and females showed a higher sensitivity to Cu (male LC50: 25.0 μg.L−1 and female LC50: 38.0 μg.L−1) than to Ni (male LC50: 90.0 μg.L−1 and female 161.0 μg.L−1) and Cd (male LC50: 127.8 μg.L−1 and female LC50: 90.0 μg.L−1). To assess for the first time, the extend of metal bioaccumulation and its effect at population scale, late stages (>200 μm) were collected and exposed to each metal at the concentration of 1/3 LC50, and to their mixture during 144 h without feeding. The Cd concentration consistently increased with time until the end of the experiment, whereas the Ni and Cu concentrations reached a plateau after 24 h and 72 h exposure, respectively. The results revealed that the copepods could accumulate Cu faster than Ni and Cd either in the treatment alone (0.58 L g−1.d−1) or in the three-metal mixture (0.72 L g−1.d−1) after 50% of exposure time (72 h). The number of individuals decreased in copepod populations except for the Cd treatment, where the number of nauplii increased. In addition, all treatments of metal exposure negatively affected bacterial densities in the copepod cultures, where the Cu treatment showed a negative remarkable effect compared with Cd and Ni treatment did.