Water environment management in Korea has long been driven by chemical water quality standards; however, such an approach does not adequately reflect the structural and functional integrity of aquatic ecosystems. Accordingly, the introduction of biological water quality criteria (biocriteria) has emerged as a key task for establishing ecosystem-centered water environmental policies. This study reviewed the scientific and legal foundations necessary for developing biocriteria suited to Korean aquatic ecosystems and proposed practical approaches for institutionalizing them as environmental standards. To this end, we conducted a comparative analysis of biocriteria implementation cases in major countries, including the United States, the European Union (EU), and Canada, and examined both the applicability and limitations of domestic multi-metric index (MMI)-based biological indicators. In addition, we evaluated the potential linkage with national legislation, including the Framework Act on Environmental Policy and the Water Environment Conservation Act, and proposed an institutionalization roadmap. This study emphasizes the necessity of establishing biocriteria as a policy turning point for securing the ecological health of Korean freshwater ecosystems and building an integrated water environment management framework.