South Korea has experienced rapid urbanization and land-use change since early 1970’s. In Korean freshwater ecosystems, impacts such as dams, estuarine barrage, and weir construction affected ecological structure and function. The evaluation of biodiversity monitoring and evaluation of change in biological communities is necessary. The Korean government has also implemented national research projects such as Korean Nationwide Survey on Natural Environments (KNSNE, since 1986), Korean National Long-term Ecological Research (KNLTER, since 2005), National Aquatic Ecosystem Monitoring Program (NAEMP, since 2007). These projects focus on floral and faunal distribution on space (KNSNE), global climate change (KNLTER), evaluating stream health (NAEMP) on freshwater biodiversity. Korean government also operates the National Institute of Biological Resources, the National Institute of Ecological Research, and the Nakdong Institute of Biological Resources for ecological research, and exhibitions and education programs focusing on freshwater biodiversity. Recently established monitoring programs and centers in Korea are excellent examples of “hardware and software” aspects of global biodiversity issue. In order to achieve outputs from these setting, scientists engaged in biodiversity research should work together toward common goals.