Freshwater ecosystems sustain biodiversity and human livelihoods but are increasingly degraded by anthropogenic pressures, necessitating reliable biomonitoring for effective management. Asa River is a key source of fisheries and domestic water in Ilorin, Nigeria, yet it is highly vulnerable to point and non-point pollution, requiring continuous ecological assessment. Previous evaluations relied solely on morphological identification of macroinvertebrates, which is constrained by taxonomic subjectivity and limited detection of cryptic taxa. This study therefore integrated environmental DNA (eDNA) metabarcoding with conventional morphology to characterize macroinvertebrates diversity to assess the ecosystem health of the Asa River based the macroinvertebrate Family Biotic Index (FBI). Sampling was conducted from 2023 to 2025. Physical and chemical variables were measured using standard methods and formulated into a Water Quality Index (WQI). Macroinvertebrate assemblages were analyzed using diversity indices, BENTIX and Biotic Index, while community patterns were explored with Non-Metric Multidimensional Scaling (NMDS) and canonical Correspondence Analysis (CCA). WQI values ranged from 89.3 to 305.5, indicating generally poor water quality. Morphological identification showed dominance of Mollusca (> 70%), whereas eDNA revealed Insecta as the most abundant group (? 38%). BENTIX scores ranged from 2.15 to 3.35, suggesting degraded ecological conditions. The NMDS indicated marked seasonal shifts in community structure, and CCA identified total phosphorus, total nitrogen and dissolved oxygen as key drivers of taxonomic distribution. The findings demonstrate eDNA metabarcoding complements, but does not replace, morphological assessment, and that integrating both approaches provide a more robust evaluation of river health. Asa River is currently dominated by pollution-tolerant taxa, reflecting its poor ecological status.