The incidence and dispersal of invasive alien fish species (IAFS) have ecological impacts on biodiversity and environmental health at regional to global scales. We identified links between the presence of largemouth bass (Lb) and bluegill (Bg), and selected indicators of environmental water quality, trophic and tolerance guilds, ecological health factors, and stream order. We used the data collected from national biomonitoring study sites in four major rivers of South Korea. IAFS occurred in eutrophic waters (Lb = total phosphorus: 140 ± 170 µg/L, chlorophyll a: 16.7 ± 27.5 µg/L; Bg = total phosphorus: 160 ± 190 µg/L, chlorophyll a: 19.43 ± 28.05 µg/L) and dominated at higher ambient ratios of total nitrogen to total phosphorus (TN:TP). At TN:TP ≤ 100, the relative abundance of Lb and Bg was highest (95.3% and 96.0%, respectively). Concerning tolerance guilds, Lb (R2 = 0.78, p < 0.0001) and Bg (R2 = 0.59, p < 0.0001) had positive relationships with tolerant species in all four river watersheds and negative relationships with the percentages of insectivores and omnivores. This indicates the harmful impacts of IAFS on the aquatic food web. These invasive fish species also influenced stream health, particularly in the Nakdong and Yeongsan/Seomjin rivers. Our findings suggest that assessing chemical water quality can help identify the optimal and suboptimal survival and spread ranges of IAFS (Lb and Bg), as they directly influence tolerance and trophic guilds in the aquatic food web. In conclusion, these IAFS could be a major factor in the deteriorating ecosystem health, which had negative relationships with the abundance and occurrence of IAFS. Therefore, approaches that use appropriate water chemistry factors and species tolerance may provide critical insights into the efficient management of river health that has been perturbed by the presence of IAFS.