Hybridization has fascinated biologists in recent centuries for its evolutionary importance, especially in plants. Hybridization outcomes are greatly affected by the environment, and hybridization is most likely in bounded or novel habitats for the parent populations. The Qinghai-Tibetan Plateau (QTP) and its adjacent regions possess extraordinarily high plant diversity, and hybridization has been shown to be an important cause. The plateau also contains numerous wetlands, accommodating diverse aquatic taxa, and we have limited information on the regional hybridization rate and pattern in aquatic macrophytes. In this study, We assessed the distribution of three related species pairs (Myriophyllum, Stuckenia and Ranunculus) and their hybrids (using chloroplast and microsatellite markers). We also evaluated the potential occurrence and niche similarity for relative parental species. The results revealed common hybridization in three pairs of ecologically divergent aquatic plants on the QTP. The drainage basins, valleys and edges of the plateau enabled sympatry of divergent taxa and contained discrete hybrid zones. Obvious niche overlap and extensive cooccurrence regions were important for the frequent hybridization. The novel and marginal niche on the QTP for aquatic plants also contributed. The hybridization patterns are different among species pairs, possibly because of differences in genetic incompatibility, niche overlap extent and phylogeographic history. Our results suggested that the QTP is a hotspot for ecologically divergent aquatic species to contact and mate and implied that hybridization may be important for the freshwater biodiversity of highlands.