A research project assessing the state of freshwater biodiversity in East and Southeast Asia was conducted from 2011-2015 to underpin the biodiversity conservation policy of the Convention on Biological Diversity. We constructed a database on the distribution of aquatic organisms and their environments, selected priority sites for conservation, and determined the anthropogenic drivers of biodiversity loss in the freshwaters of Japan. This special issue shows a portion of our findings. For lakes, more than two-thirds of selected priority sites were located in areas that were already protected; however, our assessment revealed that the species richness of both freshwater fishes and aquatic plants decreased markedly after 2001 compared with previous years. The total area of protected rivers and ponds was far beyond that proposed by the Aichi target. There were large gaps between selected sites and protected areas with rivers and wetlands. The major drivers of biodiversity loss were exotic piscivorous fishes and eutrophication in lakes and ponds, and habitat fragmentation in rivers. We found that the distribution data of indicator species were insufficient for proper assessment, and were particularly lacking in static waters (lakes, ponds, and wetlands) for the past 10-20 years.