An invasive species is defined as a biological species introduced, most often through human action, that causes direct harm, such as reducing or driving native species to extinction. This introduction can result in long-term changes to ecosystem structures and ultimately contribute to a decline in biodiversity within areas where it was not previously present. Thus, continuous monitoring and management are essential. This study examined the impact of two exotic species, largemouth bass (Micropterus salmoides) and bluegill (Lepomis macrochirus), on fish diversity in rivers across South Korea. Data from the “Stream Ecosystem Survey and Health Assessment” project, which was conducted along five major river basins between 2013 and 2021, were analyzed. The data were divided into three periods: 2013–2015, 2016–2018, and 2019–2021, covering a total of 960 sites. The results revealed that largemouth bass and bluegill were present at 360 sites (37.5%) from 2013 to 2015, 325 sites (33.9%) from 2016 to 2018, and 356 sites (37.1%) from 2019 to 2021. Additionally, when comparing sites where exotic fish were present with those where they were absent, the average number of native species was slightly higher in areas where these invasive species were present, yet the average Fish Assessment Index (FAI) value was lower. Statistically significant differences were observed in fish diversity, especially in trophic and tolerance traits. This study provides valuable insight into the impact of invasive species on South Korean river ecosystems and offers important information for developing future conservation and management strategies for biological resources.