Low light intensity and high sediment organic matter (SOM) conditions coexist recurrently in aquatic ecosystems, which affects submerged macrophyte re-habilitation. In this greenhouse study, four light intensity levels (10% [natural light intensity], 30%, 60%, and 100%) and three initial SOM loads (11% [measured as the loss on ignition], 17%, and 25%) were applied to explore the effects of their interactions on the growth of Vallisneria natans (V. natans). Two-way ANOVA revealed the effects of interactions between light intensity and SOM load on the growth characteristics of V. natans. Multiple linear regression models indicate that the dry weights and root lengths exhibited a single maximum as the SOM load increased. The inhibitory effect of the sediment on the growth of V. natans could be alleviated by increasing the light intensity in a certain SOM range. However, the inhibited growth of V. natans was not alleviated by enhancing the light intensity at a 25% SOM load. We explored a potential mechanism for this phenomenon based on ammonium (NH₄⁺) toxicity regulation. Structural equation modeling indicates that enhanced light intensity could directly reduce sediment NH₄⁺ contents or reduce them indirectly by decreasing the abundances of bacterial functional genes associated with NH₄⁺ formation. Subsequently, lower sediment NH₄⁺ content increased the plant dry weight, thereby facilitating the removal of nitrogen and phosphorus from the sediment. Therefore, enhancing the light intensity over a wide range of SOM loads resulted in the restoration of submerged macrophytes, whereas reducing SOM loads could be performed in high SOM conditions to improve the restoration of submerged macrophytes.