Biological health assessment (BHA) has developed as an imperative gauge in efficient management of freshwater resources and fish assemblages. The principal objective of this research is directed at the development and application of a new index under the umbrella of the famous index of biological integrity (IBI). Further, we intended to carry out comparative assessments of the new index with two existing indices and testified to their rational in Geum River watershed, which is the third largest river water basin in South Korea. We analyzed the biotic integrity of 149 different study sites in the streams and rivers of Geum River watershed, perusing fish assemblages and water quality data. The results revealed the newer index, i.e., multi-metric (mm) IBI 06 (mmIBI 06 metrics), as comparatively more efficient than previously used indices, i.e., mmIBI 08 and mmIBI 11. Furthermore, the linear regression and correlational analyses indicated harmonic relation of mmIBI 06 with mmIBI 08 (R2 = 0.85) and mmIBI 11 (R2 = 0.87). Nonetheless, linear regression modeling discovered a very strong positive relation between mmIBI 08 and mmIBI 11 (R2 = 0.91), thereby implying previously used indices demonstrate better approximation. In significant contrast to both old indices, the newer index exhibited improved facility to better classify the study sites between the assortments of ‘excellent to very poor’ compared to old indices elucidated one-step lower, i.e., from ‘excellent to poor’. For instance, the newer index categorized 60 sites as ‘very poor’, requiring immediate attention owing to biological degradation. Additionally, the newer index endures grander ability to indicate sites requiring immediate management or restoration attention with a plausible site classification, especially in relation to the invasive alien species (IAS). The water chemistry was mainly influenced by rampant anthropogenic actions compounded by intensive monsoon precipitation that may relinquish highly suitable grounds for invasive alien fish species. This may eventually lead to severe biological degradation and successive deterioration of habitat by the IAS. In conclusion, the newer index endures ample capacity to indicate the fish community disturbances in rivers and streams. Further, correlation, linear regression, as well as principal component analysis (PCA) analyses on biotic indices and water chemistry showed higher approximations. Therefore, our newer index would be a valuable BHA tool to classify and elucidate the streams and rivers by indicating sites necessitating preferred attention and restoration measures.