At Sede Boqer (northern Negev desert, Israel), aeolian dust dynamics have been measured during the period 1988–2000. This study focuses on temporal records of the vertical and horizontal dust flux, the vertical distribution of the dust particles in the atmosphere, and the grain size of the particles. This study extends results reported earlier on the characteristics of the airborne dust concentration, the accumulation of dust on the desert floor, and the high-magnitude dust events. Vertical dust flux showed a systematic trend over the year, with high values in spring and low values in autumn. Vertical flux was very low from 1989 to 1991 and from 1997 to 1998, and moderately high or high in the other years. Horizontal dust transport, which was quantified by means of the horizontal dust flux, was also highest in spring and lowest in autumn and in winter. During the period 1988–2000, the horizontal dust flux value oscillated systematically with a periodicity of 30 months. At Sede Boqer the amount of dust in the atmosphere always decreased with height. Vertical stratification was strongest during the first months of the year and lowest at the end of the year. Stratification was very low in 1989–1991, high in 1988 and between 1992 and 1996, and moderate in the other years. The size of the dust (quantified by means of the median grain diameter) was also highest in spring and lowest in autumn. Median grain diameter was around 30 μm in 1988–1989, in 1995–1996, and in 1999–2000; in the other years it was considerably lower, around 25 μm or less. The average annual vertical dust flux curve parallels the average annual wind speed curve. A similar relationship was observed between airborne dust concentration and vertical dust flux, but only for the background concentration. At Sede Boqer, a negative relationship exists between the amount of rainfall and the amount of vertical dust flux. This relationship is not only apparent during the rainy season itself, but also when the amount of rainfall during a rainy season is compared to the amount of vertical dust flux during the next dry season. The dust crust on the desert floor, which is much stronger after rainy seasons with high precipitation than after rainy seasons with low precipitation, is most probably responsible for the latter relationship.