Riparian vegetation is crucial for stabilizing riverbanks, improving water quality, and sustaining aquatic biodiversity by forming a transitional zone between aquatic and terrestrial systems. In the Sundarbans, the world’s largest mangrove forest, these vegetated buffers are ecologically essential for preserving delta stability, filtering sediments, and providing nursery grounds for juvenile fish in the Sundarbans. Despite growing understanding of their roles, few studies have explored how environmental gradients together affect estuarine fish resources and riparian vegetation. Therefore, using the hydro-ecological data (vegetation, fish and water) of 65 canals, this study aims to (I) asses the distribution of plant and juvenile fish community in the Sundarbans, (II) investigate the impact of habitat conditions on riparian plant and fish resources, and (III) understand the interconnection between riparian vegetation, fish community, and water conditions. This study found that the distribution of riparian plants and fish species is considerably shaped by water parameters, and a significant variation is present in three ecological zones. Additionally, the association among abiotic parameters, fish richness, and plant richness was significant, but plant richness did not show a significant relationship with fish richness. This implies that the terrestrial and aquatic biota are functionally decoupled or respond asynchronously. These results emphasize that riparian habitats can lead to complex effects on fish richness patterns and suggest the necessity of coordinated conservation strategies and the intricate and context-dependent character of riparian–aquatic interactions. . This study shows how important it is to perform integrated ecological evaluations that look at both land and water biodiversity.