The Amazon is Earth's largest river by volume output, making it an important source of trace metals and dissolved organic matter (DOM) to the Atlantic Ocean. Despite major recent anthropogenic disruptions to the Amazon catchment area, data for trace metals such as copper (Cu) in the Amazon River estuary and associated mixing plume are still rare. Furthermore, there is currently no existing data in this region for Cu-binding ligands, which govern the amount of bioavailable Cu. To understand trace metal mixing and transport processes, the GEOTRACES process study GApr11 (cruise M147 with RV Meteor) was conducted in 2018 in the Amazon and Pará River estuaries and mixing plume in the tropical North Atlantic Ocean during high river discharge. Size-fractionated surface samples were collected along the full salinity gradient for concentrations of Cu, apparent Cu-binding organic ligands (LCu) and corresponding conditional stability constants (K′CuL, Cu2+cond), electroactive humic substances (eHS), solid phase extractable organic Cu (SPE[sbnd]Cu), dissolved organic carbon (DOC), chlorophyll a (Chl a) and macronutrients. Dissolved (<0.2 μm) and soluble (<0.015 μm) Cu correlated negatively with salinity and largely followed values expected from conservative mixing. Cu was primarily in the soluble fraction, with the exception of a minor fraction of large colloidal Cu at low salinity (S ≤ 10). Organic ligands (log K′CuL, Cu2+cond = 12.6–15.6) were present in excess of Cu and likely played a role in solubilizing Cu and preventing Cu being affected by colloidal flocculation. Cu-associated DOM (measured as LCu, eHS and SPE[sbnd]Cu) correlated negatively with salinity and appeared to be primarily governed by river input and mixing with seawater. However, an increase in the colloidal fraction for LCu and eHS observed at S ~ 6–10 was attributed to possible additional autochthonous (phytoplankton) ligand production. In all dissolved samples, organic complexation kept free Cu below levels potentially toxic for phytoplankton (<1 pmol L−1). Despite increasing anthropogenic activity over the past century, we find Cu concentrations remained similar to the 1970s, suggesting that the large overall river flow may so far minimize the impact of Cu pollution.