The role of the Setúbal–Lisbon canyon in accumulation and transport of labile organic matter from the coastal sea and ocean surface water towards the deep sea was assessed by investigating the distribution of organic matter of different quality in sedimentary aggregates and surface sediments of the canyon and adjacent slopes. Total hydrolysable amino acids (THAA) and organic carbon (Corg) were measured from aggregates, and contents of Corg, chlorophyll a (chl a), phaeopigments (phaeo), chloroplastic pigment equivalents (CPE) from sediments. As indices of organic matter (OM) quality THAA:Corg, degradation index (DI), chl a:phaeo, chl a:Corg and C:N ratio were determined. Sediment profiles of chl a and the isotope 210 of lead (210Pb) were used as tracers in a transport model to estimate deposition rates and background levels of the tracers, and sediment mixing rates (Db). Whereas bulk Corg contents of canyon and slope sediments were practically similar at all depths, higher contents of THAA, chl a and CPE, as well as higher THAA:Corg, DI and chl a:Corg, in aggregates and sediments from the upper reaches of the canyon indicate that labile organic matter accumulates in the upper canyon. This is confirmed by higher chl a and 210Pb deposition and Db calculated from the model. Hence, the Setúbal–Lisbon canyon, specially the upper region, acts as a natural trap of organic matter that is transported to the region via lateral transport and vertical settling from primary productivity. Organic matter might be further transported in downward canyon direction via rebound processes. The chl a and 210Pb profiles reveal active sediment mixing by physical processes and/or animal reworking.