This paper provides an overview of the development and application of the National Aquatic Ecological Monitoring Program (NAEMP) in Korea, which uses biological and habitat–riparian criteria for river/stream and watershed management. Development of NAEMP began in 2003, with recognition by the Korean Ministry of Environment (MOE) of the limitations of applying chemical parameters (e.g., biochemical oxygen demand (BOD)) as the principal targets of water environment management. Ecosystem health criteria under NAEMP were developed from 2003 to 2006. Candidate sites for monitoring were also screened and established across the country. NAEMP was implemented in 2007, and since then a standard protocol of nationwide monitoring based on multi-criteria has been implemented to assess the ecological condition of rivers and streams. The monitoring results indicate that many Korean rivers and streams are severely degraded, with biological conditions that are much worse than their water chemistry suggests. In 2009, 24% of rivers and streams were in classes C (Fair) and D (Poor) for BOD, but more than 71, 53, and 27% were categorized as Fair to Poor according to fish, diatom, and benthic macroinvertebrate assemblages, respectively. NAEMP is promising in that the results have already had great impacts on policy making and scientific research relevant to lotic water environment and watershed management in Korea. In the future, NAEMP results will be used to develop more aggressive regulations for the preservation and restoration of rivers/streams, riparian buffer areas and watersheds. Another future aim of the NAEMP is to develop aquatic ecological modeling based on the monitoring results.