The modified material at the bottom of lakes plays a key role when restoring and reconstructing the ecology of waterbodies. However, the effects of different substrate types on the growth and development of submerged plants and rhizosphere microorganisms remain unclear. Therefore, this study analyzed the effects of five substrates (attapulgite, biochar, cinder, maifanite, and quartz sand) on the growth and rhizosphere microorganisms of Vallisneria natans (Lour.) Hara (V. natans). The results showed that during the culture period, the mean plant height of V. natans peaked in the maifanite group (26.75 cm), the mean leaf number peaked in the biochar group (12.13), and the mean root activity peaked in the cinder group (83.42 U g⁻¹ min). There was no significant difference in the total chlorophyll content among the groups during culture (P > 0.05). The malondialdehyde content of V. natans leaves in all groups, except quartz sand group, peaked early in the culture period (10 days). Moreover, the superoxide dismutase activity of the five groups increased first and then decreased; however, the catalase activity in the maifanite group decreased significantly compared with the levels in the other groups (P<0.05). This indicates that maifanite supplementation can accelerate the adaptation of V. natans to changes in the environment. After the addition of substrate, the species of dominant bacteria in the rhizosphere remained nearly unchanged, but their relative abundance was different. Specifically, the relative abundance of Desulfobacterota increased in each group, peaking at 9.77% in the maifanite group. This study showed that different substrates had different growth-promoting effects on submerged plants, with maifanite exerting the greatest effect. The findings provide a technical reference for selecting the best substrate improver for in situ ecological restoration.