This one-year survey conducted in the macrotidal estuary of Penzé (Brittany, Western part of the Channel, France) was aimed at examining the variations of the various dissolved and particulate copper species. Ten field stations along the whole freshwater–seawater mixing zone were sampled each month. Different biogeochemical parameters (SPM, chl-a, pH and DOC) were also measured. The levels in total dissolved and total particulate copper ranged from 1.8 to 9.5 nM and from 5 to 98 μg g−1, respectively; such amounts are indicative of a pollution-free system. Extractable C18 copper (non-polar hydrophobic organic copper species), in winter and spring, accounted for 30–40% of the total dissolved copper. In summer, this contribution rapidly rose to 60% in the salinity range 20–30; over the same period of time, total particulate copper decreased. The change in dissolved copper speciation and the lowering of particulate copper concentrations were attributed to the release of strong organic ligands by phytoplankton. Our field data evidenced a highly variable behaviour for the various copper species over the seasonal cycle, and then led us to identify the following mechanisms: (i) metal desorption from organic river-flown particles (winter and spring), (ii) metal desorption from resuspended sediment in the upstream section (summer), (iii) competition between particles, non-extractable C18 organic ligands and phytoplankton-released extractable C18 organic ligands to complex copper in the downstream section (summer), and (iv) removal of non-extractable C18 organic copper by adsorption (autumn). Dissolved copper species fluxes were assessed: most of metal inputs to the estuary (60–74%) corresponded to non-extractable C18 organic copper. Winter and spring metal output fluxes were mainly constituted of non-extractable C18 organic complexes; on the other hand, extractable C18 organic complexes were predominant in summer and autumn output fluxes.