Temporal variations of rare earth elements (REE) and their fractionation patterns, major elements, Pb and Hg were determined in two multicores collected at 445 and 2100 m water depth (mwd) in the Cascais submarine canyon (CSC). The PAAS-normalized REE patterns suggest mixing of Tagus estuarine and marine sediments, marked by MREE (Nd‐Dy series) enrichment and by positive Eu-anomaly, with marine sediments. The positive Eu/Eu* implies incorporation of detrital feldspar minerals derived from the estuary. Ce/Ce*, (La/Yb)_PAAS and (Nd/Yb)_PAAS show differences between the two cores. Core 252-35 from the shallower site is enriched in HREE (Ho‐Lu series) over LREE (La‐Pr series), a pattern also found in the Tagus estuary in the vicinity of an abandoned chemical complex, where the environment is affected by the legacy of massive-sulfide ores processing. There seems to be only limited down-canyon sediment transport to the deeper reaches where core 252-32 was collected. This deeper site shows Ce/Ce* peaks coinciding with low (La/Yb)_PAAS values suggesting preferential diagenetic remobilization of LREE relative to HREE. Upcore Pb/Al and Hg/C_org trends observed in both cores indicate dispersion of the anthropogenic component from the estuary through the CSC, which is less obvious from the ∑REE/Al trends particularly in the deeper site. This may suggest the influence of diagenetic processes in the REE signal, associated with relatively low sediment accumulation rates.