Natural organic matter (NOM) in aquatic environments reduces metal toxicity to fish by forming metal–NOM complexes, which reduce metal bioavailability, metal–gill binding and toxicity. However, differences in the chemical composition of different types of NOM (quality) could also affect metal–NOM binding and toxicity. We predicted that Cu–gill binding would vary in trout exposed to Cu in the presence of NOM of different qualities. NOM was collected from three sources: Luther Marsh (terrigenous ∼ allochthonous), Bannister Lake (nominally autochthonous), and from a local sewage treatment plant (designated Preston effluent). Excitation–emission matrix spectroscopy (EEMS) revealed that terrigenous Luther Marsh NOM was primarily humic acid-like material (74%), whereas Bannister Lake and Preston sewage effluent NOM had lower humic acid-like material but greater fulvic acid-like material (30% and 50%, respectively). The specific absorption coefficient (SAC) of Luther Marsh NOM was also much higher (SAC = 37.8), consistent with its darker color, compared to more autochthonous, lightly coloured Bannister Lake (SAC = 12.4) NOM, and Preston effluent NOM (SAC = 9.2). At low-moderate waterborne Cu (0–2,000 nmol L −1), all NOM isolates reduced Cu–gill accumulation by 70–90%. Surprisingly, there were no measurable differences in Cu–gill binding amongst the three NOM treatments when fish were exposed to Cu in the low-moderate range. Only at higher Cu (>2,000 nmol L −1) were differences observed, where terrigenous Luther Marsh and Preston effluent NOM reduced Cu–gill binding by 40–50% more than the more autochthonous Bannister Lake NOM. Although Cu–gill binding estimates using the HydroQual BLM showed similar trends, the BLM consistently underestimated Cu–gill binding. We conclude that differences in Cu toxicity at lower-moderate Cu concentrations in the presence of different types of NOM are not necessarily related to measurable differences in Cu–gill accumulation. Rather, we suggest that differences in Cu toxicity reported in the presence of different types of NOM might be explained by direct actions of NOM on the gills, which are quality dependent.