In this study, we assessed the characteristics of the fish community and the health of the river aquatic ecosystem of Jojongcheon Stream, a tributary of Bukhangang River in South Korea, from 2023 to 2024. We conducted surveys at 30 stations using kick nets and cast nets to sample each site twice (first survey: April~May; second survey: September~October). A total of 12 families, 42 species, and 7,105 individuals were collected. The dominant species was Zacco koreanus (52.4%), followed by the subdominant species Z. platypus (14.2%) and other notable species such as Pungtungia herzi (9.4%), Coreoleuciscus splendidus (4.1%), Rhynchocypris oxycephalus (3.7%), and Iksookimia koreensis (2.3%). The remaining species accounted for 13.9% of the fish community. Among the collected species, three were classified as second-grade endangered wildlife by the Ministry of Environment: Rhodeus pseudosericeus, Pseudopungtungia tenuicorpa, and Cottus koreanus. Of these, C. koreanus inhabited the upper reaches and tributary sites, while P. tenuicorpa and R. pseudosericeus were located in the mid- to downstream sections of Jojongcheon Stream. We also recorded 20 Korean endemic species that represent a high endemism rate of 47.6%, along with one catadromous species, Anguilla japonica, and two landlocked species, Cottus koreanus and Rhinogobius brunneus. Among the exotic species, we identified three that include two ecosystem-disrupting species-Lepomis macrochirus and Micropterus salmoides- and Cyprinus carpio (Israeli type). We noted species dominance decreased from upstream to downstream in community analysis, as diversity and richness increased downstream; There was no clear trend in evenness among the stations. The stream health was “good” (Grade B) at two stations and “very good” (Grade A) at 28 stations from the fish assessment index (FAI) scores. The water quality grading results, based on the water quality monitoring network, classified one station as “very good” (Ia), and three stations as “good” (Ib). Disturbance factors included river control works at two stations and construction of weirs at 18 stations, of which only six (33%) had fishways, hindering fish migration. Ecosystem-disrupting species such as M. salmoides and L. macrochirus were observed in the downstream sections and raised concerns about ecological disturbance. To ensure stable habitats of fish species in Jojongcheon Stream, it is pivotal to minimize indiscriminate river construction, install fishways at weirs, and develop management strategies to reduce the populations of invasive species.