To maintain performance related to fuel consumption and maneuverability, the bottom of ships are painted with antifouling paint that contains Cu2O as a biocidal pigment. However, in enclosed coastal areas around dockyards, some of the Cu(II) contained in the paint is eluted into the surrounding water. The present study examined the removal of Cu from seawater by co-precipitation with humic acids (HAs). After precipitating the HA in seawater, the amount of Cu(II) in the supernatant was colorimetrically measured by a colorimetry using bathocuproine. The removal efficiency (RE%) for micromolar Cu(II) increased with increasing initial concentrations of HAs. An RE of 90% was obtained using an HA derived from hardwood bark compost. Aromatic components in the HA that contained highly substituted acidic functional groups appeared to enhance the removal of Cu(II). The findings reported herein indicate that HAs represent a useful material for removing trace levels of Cu from seawater.