Aquatic plants are the ecological group that mainly consists of herbaceous plants with habitats that are closely associated with water. Most aquatic plants have strong clonality. In response to changes in aquatic environments, aquatic plants exhibit significant plasticity in morphological, behavioral and physiological traits, and thus adapt well to heterogeneous aquatic environments. Compared with extensive studies on phenotypic plasticity of terrestrial plants, less attention has been paid to test how phenotypic plasticity of aquatic plants responds to heterogeneous environments. In this review, we briefly clarified the major types of phenotypic plasticity and their relationships in clonal plants in heterogeneous environments, identified the uniqueness of aquatic environments in relation to environmental heterogeneity, and analyzed the theoretical possibilities of aquatic plants showing high phenotypic plasticity. Furthermore, we probed into how aquatic plants adapted to heterogeneous aquatic environments by means of phenotypic plasticity involved with morphological plasticity, foraging behavior, clonal integration, intraclonal labour division, and risk spreading. Finally, we identified shortcomings in current studies on phenotypic plasticity of aquatic plants, and highlighted some issues deserving more attention in future studies, which include: (1) the changing pattern and mechanism of phenotypic plasticity; (2) the influence of clonal integration on community and ecosystem stability; (3) the trade-offs between clonal integration and fragmentation; (4) the differences of phenotypic plasticity in different types of clonal architecture, and their mechanisms; (5) the adaptive evolution of phenotypic plasticity; (6) the interaction of aquatic plants with species in other taxa or at different tropic levels; and (7) the response of aquatic ecosystems to global change.