<p>Changes in fluvial characteristics, water flow regimes, and anthropogenic pressure have severely impacted the middle Ganga River, leading to resource scarcity for aquatic biodiversity. Despite the importance of habitat assessment in managing these ecosystems, gaps remain in understanding the process to fluvial stress factor, maintenance of minimum water to sustain Environmental flow (E-flow) and delineating potential riverine habitats for biodiversity. This study aims to identify clusters of riverine habitats. We used Geographic Information System (GIS) and Analytical Hierarchical Process (AHP) to undergo Multi Criteria Decision Making (MCDM) analysis. Weights assigned to variables based on their ecological significance, achieving a favourable consistency ratio of 0.0276 in model validation. The resulting potential habitat areas are categorized into four classes i.e., high, moderate, and low potential area along with restoration area. Key findings indicate that Ganga River from Sirsa to Kaithi has high potential habitat for aquatic biodiversity. Stretch between Jhilmil Jheel Conservation Reserve to Bijnor and Narora to Kannauj need more conservation effort for aquatic biodiversity. Particularly, stretches downstream of tributary confluences possess high potentiality for supporting species, such as the Gangetic dolphin (<i>Platanista gangetica</i>), whereas, sand bars and islands are important habitat for Smooth coated otter (<i>Lutrogale perspicillata</i>), Gharial (<i>Gavialis gangeticus</i>), Turtles and birds. River sections between barrages, particularly those lacking tributary input, are critical for species survival. This study underscores the need for effective management strategies to address fluvial stressors and enhance habitat conservation for aquatic biodiversity in the Ganga River system.</p>