Brackish water zones are areas with high ecological conservation value. In this study, 325 river estuaries in the Korean peninsula in individual sea areas (West Sea, South Sea, and East Sea) were divided into types of estuaries (upstream and downstream of open estuaries, closed estuaries) through the assessment of the health of the estuary aquatic ecosystems and fish communities were identified. An ecological assessment was carried out using the Korea Estuary Fish Assessment Index (KEFAI). The number of species increased as the size of the river increased in the case of small estuaries but gradually decreased in the case of large estuaries. In the closed estuaries, the relative abundances (RAs) of primary freshwater fish were the highest; however, in the open estuaries, the RAs of estuary fish were the highest. Non-metric dimensional analysis results suggested that there was a clear difference between the fish assemblages in the closed and open estuaries. The overall results of this study were that the RA of tolerant species was higher, and KEFAI was lower in closed estuaries than in open estuaries, indicating the negative effects of the construction of transverse structures on fish assemblages. The health of these estuarine ecosystems can be improved by addressing these negative effects.