Saudi Arabia has implemented ambitious environmental protection programs by creating numerous nature reserves throughout the country. Establishment of the latter nature reserves has led to farm abandonment and the initiation of ecosystem recovery processes. Agricultural practices are known to impact the structure and physicochemical properties of soils while also often markedly affecting natural ecosystem restoration processes. Moreover, weed proliferation in crop fields may modify soil seed banks (SSB), thereby impacting subsequent vegetation recovery. Therefore, it is essential to assess SSB compositions in degraded sites, such as abandoned farms (AF), so as to identify weed species and design efficient restoration strategies in hyperarid ecosystems. In this study, SSB compositions in upper and deep soil layers, standing vegetation compositions, and soil chemical properties were analyzed and compared for two natural ecosystems (NE), two abandoned orchards (AO), two AF, and two natural evaporite basins (EB). NE, AO, AF, and EB all exhibited similar chemical properties, suggesting that former agricultural activities have been guided by a fine understanding of the local environments. Agriculture had impacted the species composition of the observed standing vegetation and germinable SSBs, which could be partly explained by soil property modifications. The findings highlighted that SSBs would warrant detailed study prior to designing ecological restoration strategies, and that the drivers of horizontal and vertical weed dissemination in hyperarid ecosystems should also be explored to gain further insight into weed proliferation patterns and to adapt restoration strategies accordingly.