Aims and background <p>Seed germination in soil depends largely on the biotic and abiotic conditions of the soil. Compared with the relationships established between most microbial communities and pre-existing plants, the role of plant-associated microorganisms in driving seed germination, a key stage in the plant life cycle, remains insufficiently understood.</p> Methods <p>We conducted field experiments to study the effects of microbes on seed germination in a soil seed bank. Furthermore, we combined this with a microcosm study whereby microbiota inoculation into sterile soil obtained from various field plots was investigated to determine the potential connection between soil microbial communities and seed germination under different water levels.</p> Results <p>Our results indicated that there were significant differences in soil microbial community properties (diversity, composition, and network complexity) under different water levels in both field and microcosm experiments. The diversity of plants in the soil seed bank was significantly correlated with microbial taxa and network complexity. Furthermore, our microcosm study showed that seed germination proportion and plant functional traits (life form, root type, seed size, and species origin) were significantly correlated with the microbial diversity index and the relative abundance of dominant phylum. Different plants possess associated germination microbiomes, and fungal topological characteristics plays an important role in predicting seed germination.</p> Conclusion <p>The study demonstrates that plant–microbe interactions (particularly during seed germination) exert significant and predictable regulatory effects on biodiversity maintenance in wetland ecosystems, providing novel theoretical foundations for wetland conservation.</p>