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Biota of coastal estuarine habitats of tropics and subtropics are extremely vulnerable. In the study, we have investigated the role of rhizosphere process in bio-accumulation of heavy metals in fine nutritive roots of riparian mangroves at eleven sampling locations of river Hooghly. The rhizospheric sediment of river Hooghly was accumulating HMs due to the presence of organic content and anthropogenic inputs. The mean EF (2.03–8.3), Igeo (−2.27–0.71), and CF (0.62–2.53) values signifies the enrichment of HMs in sediment fine fraction (<62.5 μm) whereas, the mean PLI (0.83 to 1.18) indicates gradual environmental degradation of river Hooghly. Low BCF observed in the river Hooghly might be due to barrier to hypodermal structures and/or any prevailing mechanism of saturation of HMs. However, BCF > 1 for Al, Cu, Cr, Mn, and Zn, signifies the phyto-remediation potential of riparian mangroves to mitigate amplified global anthropogenic environmental changes. • The organic content in rhizospheric sediment regulates heavy metal accumulation. • Sediment quality indices signify the enrichment of heavy metals in sediment fine fraction (<62.5 μm). • Fine nutritive root heavy metal concentration is directly proportional to the bio-availability of metal • BCF emphasizes the phyto-remediation potential of riparian mangroves. • The study highlights the significance of region specific integrated coastal management plan [ABSTRACT FROM AUTHOR]