This study monitored the spatial and temporal fluctuations in the riverine ecosystem of Noa Dihing, Arunachal Pradesh, over three years (October 2020 to December 2023). The habitat quality of the riparian ecosystem, along with key physicochemical parameters (such as temperature, pH, dissolved oxygen, and others), organic matter composition (OMC), substrate composition, and fish species diversity, was assessed seasonally. The habscore and riverine habitat quality index (RHQI) were recorded the highest in the upstream regions (8.00 and 0.85, respectively), while OMC was the highest in the downstream (7.51). Fish biodiversity was evaluated through indices like the Shannon-Wiener diversity index, which peaked at 3.60 in the post-monsoon, and the Margalef richness index, which reached 6.61 in the same season. Simpson's dominance index showed its highest value in winter (0.7), while the evenness index was the greatest in the post-monsoon (0.90). Altogether, 46 fish species from 5 orders were recorded, with Cyprinids being the dominant group. The study utilized Duncan's multiple range test (DMRT) (P≤ 0.05) to confirm the importance of water quality in shaping fish assemblages. Principal component analysis (PCA) on physicochemical parameters explained over 60% of the total variance, with eigenvalues greater than 1.0. Species such as those from the genera Balitora, Garra, Sisor, and Oreichthys exhibited notable structural adaptations to their environment, while species like Pseudoecheneis and Glyptothorax showed thoracic modifications, and Chagunius, Garra, and Paracanthocobitis bore suctorial discs for adhesion. This comprehensive study illustrates the diverse ecological dynamics of the Noa Dihing River, emphasizing the critical role of habitat quality and physicochemical factors in influencing fish diversity and adaptation.