Distinguishing between natural and anthropogenic processes in sedimentary records from estuaries with legacy pollutants is an essential task, as it provides baselines to predict future environmental trajectories of coastal areas. Here, we have addressed the recent transformation history of the mining-impacted Nalón Estuary (Asturias, N Spain). Surface and core sediment records from marshes and tidal flats were examined through a broad multidisciplinary approach, involving micropaleontological (benthic foraminifera), sedimentological (grain-size), geochemical (trace metals, major element Al and total organic carbon), physical (magnetic susceptibility, frequency-dependent magnetic susceptibility and large microplastics) and radioisotopic (210Pb, 137Cs and 239+240Pu) proxies. Results suggest that the interplay between natural (high fluvial influence and extreme hydrological events) and anthropogenic (coal and mercury mining disposals) factors induced strong sedimentation-erosion processes, further shaping the recent evolution of the estuary. Short-time scale and intense sedimentation processes were revealed by overall high sediment accumulation rates, the dilution of some geological signatures and the rapid formation of a marsh in the lower estuary bay. The increasing mining fingerprints during the 20th century were shortly interrupted by the catastrophic riverine flooding of 1938. Conversely, current erosional processes by fluvial influence led to the remobilization of contaminated sedimentary materials and exposure of mining-legacy Hg levels in tidal flats from the middle sector. Fluvial activity, floodings and taphonomic biases exerted a major control on benthic foraminifera since the 19th century, although Hg ecotoxicological effects on modern assemblages at certain areas within the estuary cannot be discarded. These findings, along with the documented enhanced erosion of marshes with ‘trapped’ pollutants (Hg, coal microparticles and microplastics), highlight the importance of monitoring the environmental and geomorphic processes taking place in historically-contaminated estuaries. Display omitted •Natural and human driving forces interacted influencing sedimentation-erosion processes.•High sedimentation was induced by natural turbidity and mining disposals.•Extreme flooding affected sedimentary deposits impacted by mining.•Fluvial erosion caused the remobilization of mercury-contaminated tidal sediments.•Erosion of marshes containing high levels of Hg, coal microparticles and abundant microplastics should be monitored.