Root systems play a vital role in material circulation in the biosphere. Based on the two hypotheses of symmetry and self-similarity in the root system, the L-system of terrestrial plants has been well established. However, related research in aquatic plants, particularly for the dynamic root growth model, is rare. This study simulated the dynamic growth processes of a primary to secondary root structure from simple roots to complex roots of aquatic plants. The dynamic root growth model mainly includes root elongation and branching rules and determines the initial root growth direction of the intersectional angle θ and radial angle γ between the main and lateral roots. Specifically, the dynamic root growth model formulations of two representative aquatic plants, the cosmopolitan invasive aquatic plant, water hyacinth (Eichhornia crassipes), and the relatively most studied aquatic plant, Eurasian watermilfoil (Myriophyllum spicatum), were established by applying the L-system. The total length of the root system of mature E. crassipes can reach 2042.78 m, indicating that the species has a high nutrient absorption capability. This may favor resource exploitation, facilitating its competitive ability with native plants. The total length of the M. spicatum root system is 73.08 m; owing to its typical dichotomous branching, this plant has a relatively high adaptation to the aquatic environment.