Riparian areas are highly dynamic systems where the control of soil pollution might be particularly challenging. Limited accessibility to river banks and bed sediments makes reclamation operations particularly difficult in these topographical positions, in comparison to floodplains. This usually leads to the large-scale spread of pollutants following pollution episodes in riparian areas. Here, we aimed to evaluate the persistence of trace-element pollution in the soils of Guadiamar River Valley (SW Spain), a large-scale remediation after a mine-spill. We monitored topsoil along the river basin, and in different topographical positions across the river section (river channel, river banks and floodplain), 16 years after a pollution episode and subsequent remediation program. River channels and banks were identified as hotspots of soil pollution, where soluble concentrations of As, Cd and Zn were significantly higher than in floodplains. Along the basin, soil pH and carbonate content was highly variable as a result of contrasted geological background, differential loads of sulfide deposition after the accident and irregular effectiveness of the applied amendments. Cadmium and Zn showed the highest levels of long-term re-distribution from the pollution source. The results suggests that the stabilization and remediation of soil pollution in river banks and channels, often overlooked when achieving remediation works, should be a priority for land managers.