The study aims to understand the metal toxicity through the relationship between bioavailability in sediments and bioaccumulation in edible bivalves in an estuary subjected to extensive sand mining. The higher deposition of total Fe, Mn, Ni and Zn in the middle region (core M) was ascribed to estuarine processes and proximity to anthropogenic sources. EF revealed moderate to severe enrichment of Ni and Cu in sediments. Igeo showed moderate degree of pollution from Co, moderate to strong pollution from Ni and strong to extreme level of pollution from Cu. In core N, the average bioavailable concentration of Fe, Mn, Zn, Cu, Co and Ni was 1.76 %, 43.18 %, 59.14 %, 62.11 %, 60.42 % and 27.33 % respectively. The average bioavailable concentration of Fe (61.23 %), Mn (56.87 %), Cu (67.98 %), Co (69.77 %) and Ni (40.99 %) was higher in the core M as compared to core N except for Zn (56.98 %). The significant (>25.00 %) proportion of metals in bioavailable fractions in cores N and M construed their non-natural sources. Metal speciation study indicated bioavailability to fauna that likely to enhance by extensive sand mining. The level of Fe, Mn, Zn, Cu and Ni in Saccostrea cucullate, Meretrix casta and Villorita cyprinoides revealed toxicity to bivalves and probably to humans.