Inland wetlands have declined dramatically in the past century in China due to human activities (wetland drainage and agricultural intensification) and soil salinization. The Songnen Plain, as one of the important meadows and saline-sodic area of China, are facing with the vegetation degradation caused by soil salinization and farmland reclamation. Soil seed banks are an important source of regenerative material in wetland and play a critical role in the maintenance of species diversity and the reestablishment of aboveground vegetation. Understanding how soil salinization affects soil seed banks is very important for plant regeneration and biodiversity conservation because salinity often reduces the ability of freshwater species to germination. We studied the structure, density, and richness of aboveground vegetation, and soil physicochemical properties in wetlands along a soil saline-alkalization gradient in the Songnen Plain, China. We also compared the seed bank responses of different communities to saline-alkaline stress for indicating the potential of soil seed bank in wetland restoration. The result showed that the species richness and seed density in the natural wetland were significantly higher than the two farmed fields. Saline-alkaline stress restricted the seed germination and establishment of wetland species even if hydrology was restored. Soil salinity and alkalinity were related to a decrease in the density and richness of aboveground by reducing soil nutrients and seed germination of soil seed bank. Carex communities were more sensitive to saline-alkaline stress than Phragmites communities. Our study indicates that soil salinity and alkalinity, as a critical environmental filter, could drive the decline of native freshwater species, especially for certain keystone sedge species, in salt-affected wetlands. Limiting agricultural development and restoring food pulses across landscapes is necessary to alleviate soil salinization, deliver seeds and maintain the region’s freshwater vegetation in salt-affected inland wetlands.