The investigations reported here focused on the amounts of various dissolved cadmium and copper species in the whole salinity gradient of the system composed of the Loire estuary and the Biscay Bay continental shelf (France). Electrochemical labile cadmium, extractable C18 organic copper and total dissolved species of these two metals were analysed. Within the estuary, levels of total dissolved cadmium and copper ranged from 0.08 to 0.29 nM and 8.0 to 21.2 nM, respectively. These values are higher than those currently reported in metal input-free estuarine waters, but remain lower than those found in heavily industrialised environments. At the sampling stations located on the continental shelf, concentrations of total dissolved cadmium varied within 0.11 and 0.26 nM, whereas those of copper were in the range 1.7–8.0 nM. Both these series of data are higher than those reported in the literature for areas in the close vicinity of the continental shelf and in the open Atlantic Ocean. Our experimental values highlighted a non-conservative behaviour on estuarine mixing for both metals, indicative of additional metal inputs. For cadmium, the rise in concentration was particularly strong: 360%. Further to the study of labile cadmium and non-polar hydrophobic organic copper fractions, the observed elevations in concentrations were related to particle desorption phenomena or to inputs from sediments. Discharges in dissolved cadmium and copper species to the continental shelf by the Loire river were assessed as 14 and 343 kg day−1, respectively. Among them 22% of cadmium flux corresponded to labile complexes, 36% of copper constituted of non-polar hydrophobic complexes. Concerning both metals a large area of the continental shelf was affected by waters from the Loire river. No change in the partition between hydrophobic and non-hydrophobic organic copper complexes was observed in this area, contrary to the cadmium one for which changes in chemical speciation were noticeable along the salinity gradient.