Abstract: Based on field investigation, data collection, and GIS, changes in nine lake shorelines and aquatic macrophyte diversity, as well as the relationship between aquatic plant diversity and lake morphology, were investigated in the middle and lower reaches of the Yangtze River, China. Results showed that aquatic plant species diversity, coastline length, and the box-dimension in the study area decreased markedly. Correlation analysis showed that the development coefficient and the box-dimension of the lake shorelines significantly affected aquatic plant species diversity. Shoreline morphology also significantly influenced submerged, free-floating aquatic plant diversity. These results demonstrate that lake shoreline protection plays an important role in maintaining the biodiversity of aquatic plants and lake ecosystem function.