The estuary of Huelva is constituted by the common mouth of the Odiel and Tinto rivers, which are extreme cases of acid mine drainage contamination due to the Iberian Pyrite Belt, the world's largest sulfide mineral province. The drained acidic waters are subjected to seawater mixing and thus, to dilution and precipitation processes that drive the load of contaminants entering the oceanic environment. This research reports the distribution of major metal(loid)s present in the highly acidic waters across the entire Tinto and Odiel estuarine systems as they are subjected to acid mine drainage neutralization, until reaching the ocean. The datasets presented are divided in low- and high-flow periods, corresponding to dry/warm and wet/cold seasons, respectively. Iron and Al were almost entirely removed from solution with pH increase at both periods due to their precipitation as schwertmannite and basaluminite, respectively. These mineral phases also, controlled the behavior of As, Cu and Pb, which were removed from solution, with >90 % of their concentration ending up in the particulate phase due to sorption processes. However, at pH >7, As returned entirely to the dissolved phase at both sampled seasons because of desorption, similarly to Cu at the low-flow period. On the other hand, concentrations of Zn, Cd, Mn, Co and Ni in solution decreased only by dilution with seawater, with null partitioning to any sorption processes during estuarine mixing until reaching the Atlantic Ocean.