For successful conservation and restoration of biodiversity, it is important to understand how diversity is regulated. In the ecological research community, a current topic of interest is how much of the variation in plant species richness and composition is explained by environmental variation (niche-based model), relative to spatial processes (neutral theory). The Yellow River Estuary (YRE) is a newly formed and fragile wetland ecosystem influenced by both the Yellow River and Bohai Bay. Here, we applied variance partitioning techniques to assess the relative effects of spatial and environmental variables on species richness and composition in the YRE. We also conducted a species indicator analysis to identify characteristic species for three subestuaries within the YRE. Partial redundancy analysis showed that the variations in species richness and composition were explained by both environmental and spatial factors. The majority of explained variation in species richness and composition was attributable to local environmental factors. Among the environmental variables, soil salinity made the greatest contribution to species abundance and composition. Soil salinity was the most important factor in the Diaokou subestuary, while soil moisture was the most important factor influencing species richness in the Qingshui and Chahe subestuaries. The combined effects of soil salinity and moisture determined species richness and composition in the wetlands. These results increase our understanding of the organization and assembly of estuarine plant communities.