Our objectives were to examine the species composition and diversity of soil seed bank (SSB) and standing vegetation (SV), explore association between compositional diversity of SV, SSB and selected environmental factors and assess the implications of SSB on regeneration of flooded riparian vegetation in Hamedan province, Iran. We estimated the ground cover of SV and SSB composition in 90 plots (1 m × 1 m) distributed across 15 sites in the river riparian zone. We evaluated the SSB by seedling emergence method. Canonical correspondence analysis (CCA) was used in a direct gradient analysis of the SV/ SSB with the environmental factors. In total, 136 species were identified from germinated seed bank in the greenhouse and there were 131 plant species recorded in the aboveground vegetation. 31 species were observed in the SSB while they were absent in the SV, while there were also 26 species that were only present in the SV. Dominant species in the SSB were floatable seed species, i.e. Cyperus difformis and Dactylis glomerata. In addition, the results indicated a more pronounced effect of environmental factors on SV than on SSB distributions in which a higher number of environmental factors associated significantly with SV than with SSB (6 vs. 4). However, elevation, soil moisture content and total organic matter had significant effects on community distribution of both SSB and SV. The species diversity and composition evenness were significantly higher in the SSB than SV. Although, 105 species were common to SSB and SV, the mean Czekanowski similarity between SV and SSB was very low (15.5%). However, we argue that the recovery of vegetation in degraded sites can still rely on SSB. We concluded that the seed movement among plant communities through hydrochory led to a spatial homogenization of SSB, resulting in a decrease in SSB-SV similarity and an increase in SSB species diversity and compositional evenness. Differences in plant diversity and richness between the SSB and the SV are supposed to be a complementation of diversity between below- and above-ground and therefore, greater community resilience is predicted under stochastic disturbance events such as flooding in the riparian area.