Long-term observations of monthly downward particle fluxes and hourly currents and temperature were initiated in 1993 in two canyons of the continental margin of the Gulf of Lion. The goals of this survey were to estimate its contribution to the CO2 global budget and to understand the role of forcing factors in the control of present-day particle exchange across this margin. A previous statistical analysis of the long-term time series suggested that variability in the transfer of particulate matter to the deep ocean could be the result of the effect of the meandering of the Northern Current and by dense water formation in winter rather than variations in the sources of matter. Numerical simulations have been carried out to consider these hypotheses. A model is used to examine the impact of local atmospheric forcing (wind stress, heat fluxes, precipitation–evaporation budget) on the variability of the oceanic circulation and of mass fluxes within the canyons from December to April, for five consecutive years between 1996 and 2001. Results show an east-west gradient of mass export on the shelf and a positive correlation between anomalies of dense water formation rates and interannual variability of particle fluxes. However, in the eastern part of the Gulf, the simulated mass export from the shelf is not significant, even during a winter of strong convection, when the measured particle fluxes are at maxima. Moreover, although the model suggests that the dense water formation could be the major hydrodynamic forcing factor, this process is not sufficient to completely explain the space and time variations of observed particle fluxes, especially at depth.