The re-establishment of submerged macrophytes is crucial for the ecological restoration of eutrophic lakes. Water depth (light intensity) and sediment nutrient levels are key factors influencing the growth of these macrophytes. Although their individual impacts have been extensively studied, their interactive effects remain unclear. We conducted a two-factor experiment to investigate the interactive effects of different water depths (50 cm and 190 cm) and sediment nutrient levels (fertile and infertile) on the growth and morphological traits of Vallisneria denseserrulata. We found that biomass, relative growth rate, below/above-ground biomass, ramet number, and leaf number significantly increased with decreasing water depth in fertile sediments, while no significant or less pronounced changes occurred for infertile sediments. The absence or weak responses to increased light intensity in infertile sediments are likely due to photoinhibition, which may be alleviated at higher nutrient levels in fertile sediments. Additionally, V. denseserrulata, in adapting to low-light environments (deeper water), increased plant height at the cost of decreased leaf number and below-ground biomass as water depth increased in fertile sediments. Our study demonstrated significant interactive effects between water depth (light intensity) and sediment nutrient levels on the growth and morphological traits of V. denseserrulata, indicating that their response to water depth (light intensity) strongly depends on sediment fertility.