As a critical component of freshwater ecosystems, aquatic plants play an essential role in sustaining the structure, function, and stability of ecosystems. However, under global change scenarios, aquatic plants are confronted with multiple stressors, including eutrophication, climate warming, emerging pollutants, and biological invasions, which have led to a significant decline in aquatic vegetation, particularly submerged macrophytes. Based on systematic research findings accumulated over the years from the Liangzi Lake National Field Station for Scientific Observation and Research, Wuhan University, this paper comprehensively reviews the major advances in the ecology of aquatic plants and their ecosystem functions across the individual, population, community, and ecosystem scales. At the individual and population levels, we revealed the environmental regulatory mechanisms of ecological stoichiometry in aquatic plants and elucidated the adaptive strategies of clonal integration and functional traits in response to heterogeneous habitats. At the community level, we analyzed the key regulatory factors governing the relationship between biodiversity and productivity, as well as the mechanisms underlying interspecific interactions. In the field of invasion ecology, we systematically clarified the driving mechanisms of exotic aquatic plant invasions under the combined effects of environmental change and biotic interactions, and evaluated the ecological impacts of exotic plants on material cycling, epiphytic communities, and pollutant responses. In terms of genetic evolution, we comprehensively employed multi-omics approaches to uncover the phylogeographic patterns, local adaptation mechanisms, and invasion potential of aquatic plants. In the context of ecological restoration, long-term in situ monitoring and restoration practices have verified the effectiveness of submerged vegetation reconstruction in controlling internal nitrogen and phosphorus loading, and new insights into combined remediation technologies and biological regulation strategies were proposed. These studies not only deepen the theoretical understanding of the relationship between the ecological adaptation of aquatic plants and ecosystem functions but also provide an important theoretical basis and practical guidance for the conservation, restoration, and sustainable management of freshwater ecosystems.