Macrophyte habitats exhibit remarkable heterogeneity encompasses the spatial variation of abiotic and biotic components such as water condition changes, climates and anthropogenic stressors. Environmental factors have been proposed as important drivers in shaping genetic and epigenetic variation of aquatic plants, yet the linking between genetic diversity, epigenetic variation and environmental variables remain largely unclear, especially in clonal aquatic plants. Here, we applied population genetic and epigenetic analysis, in conjunction with the habitats discriminations to detail the environmental factors of which drive intraspecies genetic and epigenetic variations of Ceratophyllum demersum from a subtropical lake. Our results demonstrated that environmental factors were highly correlated to the genetic and epigenetic variation of C. demersum, temperature was a key driver in generating the genetic variation of this aquatic herb. Genetic and epigenetic variation were positively driven by water temperature, climate temperature was defined to exert negative effects on genetic and epigenetic variation. These findings indicate that the genetic and epigenetic variations of this clonal aquatic herb could not be related to the geographic feature, but driven by environmental hierarchal, which confers new benefits of temperature to local genetic and epigenetic variation in aquatic systems.