Seed banks play a crucial role in arid plant communities because they confer stability and long-term persistence. However, seed banks have high temporal and spatial variability, with dramatic changes in density and composition. The aim of this study was to test whether seasonal change affected seed bank community structure and spatial pattern. Moreover, we wanted to know if the effect driven by environmental factors on the seed bank was constant year round. We sampled the seed bank at 188 points along seven parallel transects through a gypsum system in central Spain. Soil samples were taken twice (September and April) in contiguous plots. In each plot we measured environmental parameters, including micro- and macroslope, vegetation band, shrub cover, lichen crust cover and landform. A nearly threefold decrease in seed bank density occurred between September (16,230 seeds m–2) and April (5960 seeds m–2). Seasonal changes in density varied widely among species; however, a seed bank was present for most species at both sampling dates. For several well-studied species (Lepidium subulatum and Helianthemum squamatum), seed losses were within the range of losses by emergence reported in the literature. In both seasons, seed bank composition was controlled mainly by community band and microslope. Sampling season had a significant, but minor effect on seed bank composition. Moreover, a high spatial correlation existed in terms of seed density and richness through the two studied seasons. These results show that the seed bank keeps a constant structure even under substantial variation in density.