Isotopic data collected to date as part of the GEOTRACES and other programmes show that the oceanic dissolved pool is isotopically heavy relative to the inputs for zinc (Zn) and nickel (Ni). All Zn sinks measured until recently, and the only output yet measured for Ni, are isotopically heavier than the dissolved pool. This would require either a non-steady-state ocean or other unidentified sinks. Recently, isotopically light Zn has been measured in organic carbon-rich sediments from productive upwelling margins, providing a potential resolution of this issue, at least for Zn. However, the origin of the isotopically light sedimentary Zn signal is uncertain. Cellular uptake of isotopically light Zn followed by transfer to sediment does not appear to be a quantitatively important process. Here, we present Zn and Ni isotope data for the water column and sediments of the Black Sea. These data demonstrate that isotopically light Zn and Ni are extracted from the water column, probably through an equilibrium fractionation between different dissolved species followed by sequestration of light Zn and Ni in sulfide species to particulates and the sediment. We suggest that a similar, non-quantitative, process, operating in porewaters, explains the Zn data from organic carbon-rich sediments.This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'.