In this study, a hydrodynamic model was applied to the Nazaré submarine canyon with boundary forcing provided by an operational forecast model for the west Iberian coast for the spring of 2009. After validation, a lagrangian transport model was coupled to the hydrodynamic model to study and compare the transport patterns of three different classes of organo-mineral aggregates along the Nazaré canyon. The results show that the transport in the canyon is neither constant, nor unidirectional and that there are preferential areas where deposited matter is resuspended and redistributed. The transport of the larger class size of organo-mineral aggregates (2000 μm and 4000 μm) is less pronounced, and a decrease in the phytodetrital carbon flux along the canyon is observed. During the modelled period, the Nazaré canyon acts as a depocentre of sedimentary organic matter rather than a conduit of organo-mineral aggregates to the deep sea, as has been reported by other authors. The results of this study are crucial for the understanding of the oceanic carbon sequestration at the continental margin, and therefore important for evaluating the role of submarine canyons within the global carbon cycle.