In arid rangelands, soil seed bank characteristics vary with rainfall patterns, livestock pressure and habitat heterogeneity. We investigated this issue by assessing spatio-temporal patterns in soil seed bank density and richness in a degraded (heavy grazing) and non-degraded (light grazing) Nama Karoo ecosystem. To account for variation in seed distribution, different microsites were compared, and the effect of diaspore size on the patterning analyzed. Long-term heavy grazing increased seed densities and species richness of the soil seed bank by favoring small-seeded and tiny-seeded annual species. The spatial patterning of the soil seed bank was, however, similar to that found under sustainable grazing. The overall seed distribution was dictated by the small-scale environmental heterogeneity, which interacted with diaspore size. Our results suggest that the degraded environment is still efficient in controlling secondary dispersal and retaining seeds. This is through low stature barriers like surface rocks, which replace the function of grazing-sensitive perennial grasses in trapping and storing small diaspores. Soil seed banks were persistent and accumulated readily-germinable seeds over time. Observed temporal pattern across the study sites indicates that both condition and sequence of preceding rainfall seasons are likely to have a profound effect on soil seed banks of subsequent years.