This work demonstrates the capabilities of nanoscale secondary-ion mass spectrometry, using the Cameca NanoSIMS50 ion microprobe, to detect and image the copper-ion distribution in microalgal cells exposed to nanomolar and micromolar copper concentrations. In parallel to (63)Cu(-) secondary-ion maps, images of (12)C(-), (12)C(14)N(-), and (31)P(-) secondary ions were collected and analysed. A correlation of (63)Cu(-) secondary-ion maps with those found for (12)C(14)N(-) and (31)P(-) demonstrated the possible association of Cu with cell components rich in proteins and phosphorus. The results highlighted the potential of NanoSIMS for intracellular tracking of essential trace elements such as Cu in single cells of the microalga Chlorella kesslerii.