An estuary is an area where a freshwater river or stream meets the ocean. Even before the importance of the value of estuaries was recognized, the estuary was lost because of large-scale conversion by draining, filling, damming, and dredging. In South Korea, 643 estuaries are located, and the total area is 3,248,300 ha, accounting for 32.5% of the total area of South Korea. Over 35% of Korean estuaries are closed estuaries which are only temporally connected with the sea, either permanently or periodically. Since 2008, in order to preserve the estuary ecosystem and solve major issues in the estuary by accumulating knowledge about the estuarine ecosystem, the Ministry of Environment of Republic of Korea has been conducting the “Estuarine Ecosystem Monitoring and Assessment Project”. At 668 sites of 325 estuaries, epilithic diatom, benthic macroinvertebrate, fish, and vegetation are investigated, and the habitat condition of each site is evaluated using the newly developed biotic index. More than 100 researchers annually record 2,097 species of estuaries according to the standardized survey guidelines over the past 14 years and provide strictly managed data necessary for establishing estuaries conservation policies. As a result of bibliometric analysis of 1,195 research articles related to the monitoring and assessment of the estuarine ecosystem, research on pollutants such as heavy metals and sediment control have recently been conducted. “Estuarine Ecosystem Monitoring and Assessment Project” is an ecological monitoring type of long-term mandated monitoring that is usually focused on identifying trends. Although it is difficult to identify the mechanism influencing a change in an ecosystem through long-term mandated monitoring, providing empirical data for supporting evidence-based policy, decision-making, and the management of ecosystems. In order to increase the efficiency of the project, research to investigate the relationship between sediments and pollutants and organisms can be conducted at specific estuaries or sites to compensate for the shortcomings of mandatory monitoring.