While freshwater ecosystems provide ecosystem services essential to human well-being, such as provisioning of water and fishery resources, they are the most vulnerable to human disturbances. The ancient Lake Biwa, which is considered one of the most important lakes for biodiversity conservation in Asian region because of its high biodiversity and endemism, has been also exposed to environmental alteration due to human activities in its watershed during the last half century. Although we have great concern about the recent biodiversity loss in this lake, it remains highly unknown what kind of human disturbances have threatened populations of which taxa and consequently how biological organization has changed historically. As the first step toward drawing up the conservation program, we gathered data on long-term changes in aquatic biota and human land uses based on GIS for the pass analysis to examine drivers for the biodiversity loss as well as for the complementary analysis to propose a minimum set of complementary landscape as protected areas. In this talk, we will present preliminary results of these analyses.