The hydrographically different conditions characterising the Western Iberian Margin (NE Atlantic) and the Gulf of Lions (Mediterranean) may play an important role in determining the biogeochemical characteristics of the sediments. To investigate this, we compared the Nazaré and Cap de Creus canyons, and their respective adjacent open slopes in terms of the organic carbon (Corg) contents, chlorophyll-a (chl-a) concentrations, C:N and chl-a:phaeopigment ratios, and also in terms of modelled mixing intensities, chl-a and 210Pb deposition and background concentrations in sediments. Chlorophyll-a and 210Pb profiles were fitted simultaneously with a reactive transport model to estimate mixing intensity, deposition and background concentrations. Further, to account for the possibility that the decay of chl-a may be lower in the deep sea than in shallow areas, we estimated the model parameters with two models. In one approach (model 1), the temperature dependent decay rate of chl-a as given by Sun et al. [Sun, M.Y., Lee, C., Aller, R.C. (1993) Laboratory Studies of Oxic and Anoxic Degradation of chlorophyll-a in Long-Island sound sediments. Geochimica et Cosmochimica Acta, 57, 147–157] for estuaries was used. In the other approach (model 2), an extra parameter was estimated to derive the chlorophyll-a degradation rate. An F-test, taking into account the different number of parameters in the models, was used to single out the model that significantly fitted the data best. In most cases, the model parameters were best-explained with model 1, indicating the empirical relationship by Sun et al. (1993) is a valid means to estimate the chlorophyll-a degradation rate in deep sea sediments. To assess the robustness with which the model parameters were estimated we provide a first application of Bayesian analysis in the modelling of tracers in sediments. Bayesian analysis allows calculating the mean and standard deviation for each model parameter and correlations among parameters. The model parameters for stations for which 210Pb and chlorophyll-a profiles were available were robustly fitted as evidenced by an average coefficient of variation of 0.22. Corg contents, chl-a concentrations, chl-a:phaeo ratios, mixing intensities, depositions and background concentrations of chl-a and 210Pb indicated that the Cap de Creus canyon and adjacent slope were less active in terms of organic matter accumulation and burial than the Nazaré canyon and respective open slope.