Aquatic plants represent a specific evolutionary group that underwent multiple independent transitions from land to water. Compared with plant terrestrialization, the genomic dynamisms underlying aquatic adaptation remain largely unexplored. Here, we assembled high-quality genomes for eight aquatic species, including two freshwater-emergent, three freshwater-submerged, and three seagrass species. Incorporating comparisons of 122 vascular plant genomes, microscopic observations, and transcriptomic profiling, we pinpointed convergent genomic features underlying aquatic adaptations. Aquatic plants (especially freshwater-submerged species) were characterized by notably accelerated evolutionary rates compared with their terrestrial relatives, arguing against aquatic habitats having slowed down evolution. Unlike previous ideas of overrepresented gene loss but limited gene expansion, we revealed substantial co-expansion events in various aquatic lineages. The detailed gene-expansion pattern highlighted the distinct adaptive strategies of freshwater-submerged species compared with seagrasses. Beyond that, we uncovered entirely diverged transcriptional responses between freshwater-submerged and emergent/floating species when waterlogged, which provides new clues for improving crop flooding tolerance.