Inland wetlands have declined dramatically in the past century due to land drainage, agricultural intensification and soil saline-alkalization in China. Soil seed banks can be an important component of ecological restoration of farmed wetlands if seeds of aquatic species can survive cultivation. To explore the response of soil seed bank to farming and accompanied environmental stress, we compared the structure and composition of seed banks between natural sedge meadows and adjacent soybean and paddy fields under two water levels (moist and flooded) and two salinity treatments (non-saline-alkaline and saline-alkaline stress) in the Songnen Plain, China. We found that the species richness and seed density in the natural wetland were significantly higher than the two farmed fields. Carex species that are dominant species in the natural sedge meadows were seldom present in the soil seed banks. Instead, other high productive species (e. g. Echinochloa crusgalli and Typha angustifolia) survived cultivation as seeds in the farmed fields. Redundancy analysis identified that soil pH, soil salt content and soil water content explained most variance in seed bank composition. Saline-alkaline stress restricted the seed germination and establishment of wetland species even if hydrology was restored. This study indicates that seed limitation and saline-alkaline stress of soil together restricted seed germination and natural restoration potential in the Songnen Plain. In addition to hydrological regulation, the active revegetation of tussock sedges, and improvement of soil saltine-alkaline condition are necessary to support regional biodiversity in the inland wetlands.