To assess the characteristics of fish communities and the health of the aquatic ecosystem in the mid-lower (mainstream) reaches of the Seomgang, 15 survey stations were selected and surveyed twice between May and August 2021. The survey yielded 5,443 individual fish representing 45 species across nine families. The dominant species was Zacco platypus (relative abundance of 41.4%), the subdominant species Z. koreanus (13.6%), followed by Coreoleuciscus splendidus (9.7%), Pungtungia herzi (6.6%), Gobiobotia macrocephala (6.3%), G. brevibarba (4.3%), Microphysogobio yaluensis (2.3%), Rhinogobius brunneus (2.0%), Acheilognathus yamatsutae (1.7%) and A. lanceolata intermedia (1.6%). Among the legally protected species, four—G. macrocephala, G. brevibarba, Rhodeus pseudosericeus, and A. signifer—were classified as endangered wildlife (class II) by the Ministry of Environment. G. macrocephalawas particularly abundant in fast-flowing riffles of the lower reaches, where gravel was prevalent, while G. brevibarbawas mostly found in similar habitats in the upper and middle-lower reaches, characterized by boulders and cobbles. Only one individual each of R. pseudosericeus (St. 12) and A. signifer (St. 15) was collected at their respective stations. The study also identified 20 endemic species in Korea, resulting in an endemism rate of 44.4%, and two ecologically concerning invasive species, Micropterus salmoidesandLepomis macrochirus. The fish-based aquatic ecosystem health index (FAI) was rated as very good (A) at 10 stations and good (B) at 5 stations, indicating generally favorable conditions. Water quality was primarily assessed as good (Ib) or slightly good (II), though it deteriorated after the confluence with Wonjucheon, which exhibited moderate water quality (III). Cluster analysis revealed that the environmental factors at the study stations were generally similar, with most classified as a Bb type, characterized by the repeated occurrence of riffles and pools. However, significant differences were noted in water depth, elevation, water width, and the ratio of riverbed materials (boulders, pebbles, gravel). Elevation and the proportion of boulders tended to decrease from upstream to downstream, while the proportions of gravel increased. These environmental factors, along with water quality, significantly influenced species distribution. The cluster structure divided the stations into three groups: upper (St. 1, 3), mid (St. 2, 4-8, 11), and lower (St. 9-10, 12-15). Identified disturbance factors included river improvement works (one station), the installation of a weir (two station), the presence of invasive species (M. salmoides and L. macrochirus), and disturbances to riffle habitats—key areas for the endangered G. macrocephala—caused by off-road vehicles in the lower reaches (St. 15). To ensure stable fish habitats in the middle-lower (mainstream) reaches of the Seomgang, it is crucial to avoid indiscriminate river engineering, improve water quality in Wonjucheon, implement management measures to prevent the spread of invasive species (M. salmoidesandL. macrochirus), and restrict off-road vehicle access in the lower Seomgang (St. 15).