The distribution and behaviour of Cu and Mo in interstitial waters collected from Cu- and Mo-rich mine tailings and natural sediments in Rupert and Holberg inlets (Vancouver Island, British Columbia) are discussed. Dissolved Fe, Mn, , and Σ H2S distributions and solid-phase Cu, Mo, Mn, and organic carbon data are used to constrain the interpretation of Cu and Mo diagenesis in both tailings and natural sediment facies. Cu is released to solution at or near the sediment–water interface in both facies either by decomposing labile organic material or as a probable result of oxidation of sulphide minerals within the tailings. Mo is significantly enriched (up to 0.6 μmol L−1) in tailings pore water, probably as a result of dissolution of soluble Mo oxides produced initially by oxidation of MoS2 during milling of the ore.In natural sediments, both Cu and Mo are removed from solution at depth, probably by precipitation as their sulphides or in solid solution with an iron sulphide phase. Similar reactions appear to be occurring at depth in the tailings. The benthic flux of copper from the tailings into overlying seawater is similar in magnitude to that observed in natural sediments; there is no indication from the present data that remobilization of copper from the tailings is perturbing the pre-mine Cu distribution in Rupert Inlet. Unlike that of Cu, the benthic flux of Mo is unique to the tailings but is insufficient to produce a measureable anomaly in inlet waters because of the short water residence time and the relatively high Mo concentration characteristic of seawater.