The release of potentially toxic metals, such as copper (Cu), into the water column is of concern during polymetallic nodule mining. The bioavailability and thus toxicity of Cu is strongly influenced by its speciation which is dominated by organic ligand (L) complexation in seawater, with L-complexes being considered less bioavailable than free Cu2+. The presence of CuL-complexes in deep-sea sediments has, however, not been systematically studied in the context of deep-sea mining. We thus analyzed the Cu-binding L concentration ([L]) in deep-sea pore waters of two polymetallic nodule provinces in the Pacific Ocean, the Peru Basin and the Clarion-Clipperton-Zone, using competitive ligand equilibration–adsorptive stripping voltammetry. The pore-water dissolved Cu concentration ([dCu]) ranged from 3 to 96 nM, generally exceeding bottom water concentrations (4–44 nM). Based on fitting results from ProMCC and Excel, Cu was predominantly complexed by L (3–313 nM) in bottom waters and undisturbed pore waters. We conclude that processes like deep-sea mining are unlikely to cause a release of toxic Cu2+ concentrations ([Cu2+]) to the seawater as > 99% Cu was organically complexed in pore waters and the [Cu2+] was < 6 pM for 8 of 9 samples. Moreover, the excess of L found especially in shallow pore waters implied that even with a Cu release through mining activities, Cu2+ likely remains beneath toxic thresholds.