Invasive alien fish species (IAFS) influence recipient ecosystems in multiple ways, from altered native fish communities to poor ecological health and higher economic losses to control and eradication. We tested key drivers and connections between an IAFS (Micropterus salmoides) presence, absence, geomorphological, hydro-chemical, physical habitat, native fish assemblages, and large river basins biotic integrity during 2016–2019. A total number of 62,121 individuals (TNI) representing 74 fish species were observed, out of which 68 species (45,677 TNI) belonged to the Geum River (GR) basin, while 63 species (16,444 TNI) were from the Mankyong/Dongjin River (MDR) basin. The results illustrated a significant contrast based on stream order, catchment area, altitude, stream gradient, and width among the sites with and without largemouth bass. However, fluctuations in nutrients (nitrogen and phosphorus) were not affected by variations in pH, dissolved oxygen, conductivity, suspended solids, and river flow. The largemouth bass has emerged as the 8th largest fish population in the GR and swiftly occupies the MDR basin with a constancy value of 45.5. Native sensitive (r = −0.38), insectivore (r = −0.252), carnivores (r = −0.085), and TNI (r = −0.512) displayed a negative correlation with increasing largemouth bass abundance. Largemouth bass induced significant regime transformation in the carnivore species. A significant difference (p < 0.01) of biotic integrity was illustrated among the largemouth bass population sites. A conspicuous interplay between ‘poor’ ecological health (r = 0.33, p = 0.038, n = 41) sites and ‘fair–excellent’ (r = −0.38, p < 0.001, n = 622) sites as compared to the overall ecological health linked with largemouth bass abundance (r = −0.397, p < 0.001, n = 663) alluded to stronger impact of the IAFS. In conclusion, the largemouth bass has potentially altered the native fish assemblage and ecological health. Further, we conclude that rapidly shifting flow patterns supported by the expanding anthropogenic interventions (weirs and dam) are the most approving factors of impending fish invasions.