Atmospheric deposition is one of the major sources of nutrients bringing trace metals to remote marine biota. In this study, total atmospheric deposition and crustal aerosol concentrations were monitored at Kerguelen Islands (49°18′S; 70°07′E) in the Southern Ocean during a short campaign in early 2005 and then continuously for about 2 years (2009–2010). Results show very low levels of atmospheric dust and trace metals concentrations but higher deposition fluxes than expected. The averaged total dust deposition flux as derived from Al deposition measurements is 659 μg m−2 d−1. Simultaneously measured Fe and Co deposition fluxes are respectively 29 μg m−2 d−1 (520 nmol m−2 d−1) and 0.014 μg m−2 d−1 (0.24 nmol m−2 d−1), giving typically crustal elemental ratios to Al of 0.54 and 2.6 10−4. Measured dust deposition is in relatively good agreement with those simulated by current atmospheric models, but suggest that previous indirect calculations from field experiments are too low by a factor of 20. Observations and model results show that dust is transported above the marine atmospheric boundary layer to Kerguelen Islands, and thus that surface concentrations are not representative of the total dust column. Indeed, using surface concentrations leads to very large computed wet scavenging ratios, and to the conclusion that it is not appropriate to derive deposition fluxes from surface concentrations at remote ocean sites.