To elucidate changes in fish fauna, fish community characteristics, and river ecosystem health in the midstream region of the Imjin River (comprising the midstream Imjin River and lower Hantan River), fish surveys were conducted twice at nine stations during May to August 2024. During the survey period, a total of 4,333 individuals belonging to 48 species, 12 families, and 5 orders were collected. The dominant species was Zacco platypus (relative abundance, 27.0%), followed by the subdominant species Acheilognathus yamatsutae (8.3%). Other abundant species included Pungtungia herzi (7.6%), Gobiobotia brevibarba (7.5%), Coreoleuciscus splendidus (6.7%), Rhinogobius brunneus (4.4%), A. lanceolata intermedia (3.6%), Microphysogobio yaluensis (3.3%), G. macrocephala (3.3%), and A. rhombeus (3.1%). Among the species collected, legally protected species included one Natural Monument species, Hemibarbus mylodon, and five Class II Endangered Wildlife species, namely A. signifer, Pseudopungtungia tenuicorpa, H. mylodon, G. macrocephala, and G. brevibarba. A total of 21 Korean endemic species were recorded, accounting for 43.8% of the total species collected. Migratory fishes comprised one catadromous species, Anguilla japonica, and one amphidromous species, Plecoglossus altivelis. The only exotic species collected was Micropterus salmoides, which is designated as an ecosystem-disturbing species in Korea. River ecosystem health assessed using the Fish Assessment Index (FAI) was rated as Excellent (A) at five stations, Good (B) at three stations, and Fair (C) at one station, indicating overall favorable ecological conditions. Water quality was classified as Good (Ib) at six stations, Slightly Good (II) at two stations, and Poor (V) at one station. While the main channel generally maintained good water quality, tributary streams exhibited poorer conditions, with Sincheon showing the lowest water quality (Grade V). Community analysis indicated relatively low dominance (0.22–0.62) and high diversity (1.89–3.05), evenness (0.70–0.84), and richness (2.32–5.62). The fish community showed a single cluster. Fish fauna in the midstream region of the Imjin River was substantially altered by habitat disturbance associated with the construction of Gunnam Dam and Hantan Dam. However, gradual recovery has been observed since the completion of these projects. The present study recorded 48 fish species, including five endangered species, indicating a recovery of the aquatic ecosystem. In contrast, the inflow of the poor-quality waters of Sincheon Stream is considered to negatively affect the water quality and ecological health of both the Hantan and Imjin Rivers. Therefore, improvement of water quality in Sincheon Stream should be prioritized, and excessive river modification and construction activities should be minimized to maintain stable fish habitats and promote ecosystem recovery in the midstream region of the Imjin River.