1. Altitudinal diversity of terrestrial plants has been widely studied, whereas little is known for the patterns of aquatic plants. Here, we used a standardised field dataset to quantify the altitudinal patterns in the diversity and structure of aquatic plant assemblages, as well as the relationships between diversity indices and environmental variables. 2. Large-scale field investigations were carried out in 128 sites ranging from 2,280 to 5,020 m above sea level across the southern part of Qinghai-Tibet Plateau, China. In total, 102 species of aquatic plants were recorded, belonging to 67 genera, 31 families. Five taxonomic, phylogenetic, and functional indices were calculated for each collection site. We firstly examined altitudinal patterns of these diversity indices, then quantified the variations of indices across water areas, water flow, and soil matrix, respectively. We also explored the relationships between diversity indices and environmental variables using redundancy and variance partitioning analysis, to detect the ecological variables that drove the diversity. 3. The results showed that taxonomic, phylogenetic, and functional diversity of aquatic plants decreased with increasing altitude. Net relatedness index of aquatic plants showed a hump pattern along the altitude gradient, with a peak around 3,800 m above sea level. There was no obvious trend in the net functional relatedness index of aquatic plants with altitude. Annual mean temperature was the most important variable associated with the taxonomic, phylogenetic, and functional diversity. Water area and water flow were significantly associated with functional structure, but not phylogenetic structure. Soil matrix also correlated with aquatic plant diversity. 4. A large-scale altitudinal gradient can influence aquatic plant diversity. Environmental filtering and niche convergence might have played dominant roles in the increasing and decreasing stages of phylogenetic structure of aquatic plant assemblages, respectively, along the altitudinal gradient. Phylogenetic and functional structure of aquatic plant assemblages showed different patterns along the altitudinal gradient, and the environmental variables better explained the change of functional structure than did the phylogenetic variables. 5. This is the first comprehensive study on the species, phylogeny, and function of aquatic plant assemblages along a large-scale altitudinal gradient. We found an altitudinal decline in the diversity of aquatic plants and different patterns in the phylogenetic and functional structures of aquatic plant assemblages. These findings indicate that functional traits have high phenotypic plasticity and are more affected by environments than phylogenetic relationships which are mainly shaped by evolutionary processes.