Effects of applying composted aquatic plants on soil chemistry, soil microbes (fungi and bacteria), and the growth of cultivated plant were demonstrated. To identify drivers promoting cultivated plant growth on soil amended with composted aquatic plant, empirical data of pot experiments were incorporated into structural equation models by hypothesizing causal relationships between the application of composted aquatic plants, soil chemistry, soil microbes, and cultivated plant growth. Cultivated plant growth, total carbon content, and bacterial and fungal richness in soil increased on soil applied with composted aquatic plants, and the composition of bacterial and fungal assemblages in soil were significantly different among the application treatments. Structural equation models explicitly demonstrated the relative importance of bacterial assemblages compared to soil chemistry as a promoter of cultivated plant growth in response to the application of composted aquatic plants. The present study is the first to demonstrate that the positive effects of composted aquatic plants on terrestrial plant growth are mediated by soil microbial processes. Our results could provide basic insights into the transfer and cycling of nutrients from aquatic to terrestrial systems through human activities.