The analysis of the aeolian content of marine cores collected off the coast of the Atacama Desert (Mejillones Bay, Chile) suggests that marine sediments can record inter-annual to inter-decadal variations in the regional southerly winds responsible for particle entrainment at the surface of the nearby desert. However, the establishment of a simple and direct correlation between the sediment and wind records is complicated by the difference of time scales between the erosion and accumulation processes. The aim of this work is to: (i) assess the inter-annual variability of the surface winds responsible for the sand movements; and (ii) determine whether the integration over periods of several months completely smoothes the rapid changes in characteristics of the transported and deposited aeolian material. To accomplish this aim, 14 years of 10 m hourly wind speed, measured at the Cerro Moreno (Antofagasta) Airport between 1991 and 2003 and at the Orica Station between 2000 and 2004, were analyzed. For each year, the wind speed statistical distribution can be represented by a combination of two to three Weibull functions. Winds of the lowest Weibull mode are too weak to move the sand grains at the surface of the pampa; this is not the case for the intermediate mode and especially for the highest speed mode which are able to erode the arid surface and transport particles to the bay. In each individual year of the period of study, the highest speed mode only accounted for a limited number of strong erosion events. Quantitative analysis of the distribution of the friction velocities and of their impact on erosion using a saltation model suggests that, although all wind speeds above threshold produce erosion events, values around 0.45 m sec-1 contribute less to the erosion flux. This gap allows separation of the erosion events into low and high saltation modes. The correlation (r = 0.997) between the importance of the third Weibull mode and the extent of higher rate saltation indicates that the inter-annual variability of the erosion at the surface of the pampa, as well as the transport of coarse particles (>100 mu m), are directly related to inter-annual variations in the prevalence of the strongest winds. Finally, a transport and deposition model is used to assess the possible impact of the wind inter-annual variability on the deposition flux of mineral particles in the bay. The results suggest that inter-annual differences in the wind speed distributions have a quantifiable effect on the intensity and size-distribution of this deposition flux. This observation suggests that a detailed analysis of the sediment cores collected from the bay could be used for reconstructing the inter-annual variability of past winds.