Paddy levees form networks of narrow linear habitats and play various roles in cultural landscapes. Traditional landscapes on the west side of Lake Biwa consist of paddy field terraces and both “stone” and “soil” levees that have been maintained by paddy field management using local resources. Paddy levees in this study site are principally classified into five different types. Our study points out how differences in paddy levee structure as well as in management practices influence the plant species. Seventeen paddy levee transects were split into four habitat types based on their species components by TWINSPAN. Spatial characteristics and physical structures of paddy levees depended on natural conditions and human activities. The species–area curves of each levee type showed a clear distinction: the “soil”, “stone” and “abandoned” curves were steep, while the “concrete” and “consolidated” ones were gentle. The vegetation on “consolidated” levees was utterly different from the vegetation on traditional levee types from the aspect of species richness and species components. “Soil” type levees contained various woody plant species and included more diverse and indigenous plant species than “abandoned” type levees.