Aquatic plants are essential for maintaining the diversity and stability of the lake ecosystem. Compared with terrestrial plants, the processes of carbon isotopes (δ¹³C) chemical fractionation in aquatic plants are more complicated. In order to get a comprehensive and systematic understanding of the processes of carbon isotopic fractionation in aquatic plants and its applications in environmental study, the relevant studies were reviewed. This paper introduced the mechanisms of carbon isotope fractionation and its influencing factors. Besides, the application of aquatic plants carbon isotope in lake ecosystems and palaeoenvironments was also summarized. Previous studies indicated that carbon sources utilization and water parameters are key factors affecting the δ¹³C of aquatic plants. And, there are differences in selecting of organic components of plants when using δ¹³C of aquatic plants to study lake environmental changes at different time-space scale. The selection of proper component is crucial for interpreting the relationship between δ¹³C in the aquatic plants and environmental changes. Taking the typical macrophytes in Taihu Lake as an example, we analyzed the values of δ¹³C in different components of macrophytes and its response to environmental changes. The results showed that there was significant difference of δ¹³C among different components of aquatic plants and their response to environmental factors. Therefore, it is necessary to select proper components of aquatic plants for analyzing δ¹³C to study the environment changes in lakes.