Mangroves occur in tropical and subtropical regions, including harsh arid areas. Little is known about how the environmental conditions of deserts influence the ecology of mangrove seedlings. The seedlings of the mangrove Avicennia marina were examined in situ in a natural stand of the southern Red Sea coast of Saudi Arabia to (1) estimate and compare the growth rate of A. marina between selected microhabitats with different tidal exposures, and (2) examine the influence of sandstorms on the growth and survival of the seedlings. Samplings were conducted in four zones established according to their tidal exposure: low tidal exposure (Z1), medium tidal exposure (Z2), high tidal exposure with numerous burrows (Z3), and high tidal exposure with a few or no burrows (Z4). Vertical growth and mortality of the seedlings and selected environmental variables were quantified. The results show that seedling growth rates differed significantly between the sampling zones, the highest growth being found in the high tidal regions (Z3 followed by Z4) and the lowest growth in Z1. Growth rate followed a significant decreasing pattern over time, coinciding with increasing air temperature and decreasing relative humidity. Sandstorms showed a marked increase in July, leading to massive dust deposition that caused extensive mortality of the seedlings by burial. Our study highlights that seedling growth can be affected by the extent of tidal inundation and that sandstorms act as a natural stressor.