Abstract. 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. After validation, a Lagrangian transport model was coupled to the hydrodynamic model to study the transport patterns of the organo-mineral aggregates along the Nazaré canyon comparing three different classes of organo-mineral aggregates. The results showed that the transport in the canyon is neither constant, nor unidirectional and that there are preferential areas where suspended matter is resuspended, transported and deposited. The results showed that the transport of the larger size classes of organo-mineral aggregates is less pronounced, and that there is a decrease in the phytodetrital carbon flux along the canyon. The Nazaré canyon acts as depocenter of sedimentary organic matter and the canyon is not a conduit of organo-mineral aggregates to the deep sea.