The aquatic plants in wetlands have been threatened by increasing human disturbances in recent decades. The present study investigates to what extent human disturbance affects the community composition and richness of aquatic plants in 3 different wetland types in Lake Tana, Ethiopia. We selected twelve wetlands representing 3 different wetland types (four lacustrine, four river mouth, and four riverine papyrus wetlands) and collected data on aquatic plant species richness and community composition, major local environmental variables, and the degree of human disturbance at multiple plots along three transects in each wetland during the dry and wet season of 2018. The unique and shared contributions of human disturbance, local environmental variables, and wetland type on variations in community compositions of aquatic plants in wetlands were investigated using variation partitioning analyses. The Overlap and Decreasing Fill (NODF) metric was used to estimate the nestedness in aquatic plant communities. A total of 113 aquatic plant species, belonging to 38 families, were identified across all wetlands during the dry and wet season. Wetland types explained the greatest proportion of variation in community composition, followed by human disturbance and local environmental variables. The species richness was negatively correlated with the overall degree of human disturbance, while NODF was positively correlated. Irrespective of the degree of human disturbance, papyrus swamps had systematically the highest species richness and supported clearly different plant communities, therefore conservation efforts should focus on these habitats. In addition, measures should be taken to restore the highly disturbed and species-poor river mouth wetlands.