Mudflat sediment cores from lower (C-1), middle (C-2), and lower regions of upper (C-3) Chapora Estuary were investigated for grain size composition, total organic carbon, total and bioavailable Fe, Mn, Cu, Co, Ni, and Zn to assess metal contamination. Accumulation of metals by Saccostrea cucullata was studied to understand metal toxicity. In core C-1, Fe, Mn, Cu, Co, Ni, and Zn showed an average concentration of 1.73%, 648ppm, 12ppm, 12ppm, 16ppm, and 25ppm, respectively, while core C-2 revealed their average concentration as 1.34%, 709ppm, 10ppm, 11ppm, 13ppm, and 28ppm respectively. In core C-3, an average concentration of Fe, Mn, Cu, Co, Ni, and Zn was 1.72%, 907ppm, 14ppm, 13ppm, 18ppm, and 31ppm respectively. Metals in sediments varied within the estuary due to hydrodynamics, discrepancies in metal sources and sand mining-induced remobilization of metals. Correlation and principal component analysis revealed Fe oxides as the key regulator of trace metal distribution in sediments along with clay and total organic carbon. Enrichment factor (EF) and geo-accumulation index (Igeo) showed more or less moderate contamination of Mn in core C-3. Also, the potential contamination index (PCI) indicated moderate contamination of Mn in core C-3 using the shale value as background concentration, whereas the application of upper crustal value revealed moderate contamination of Fe, Mn, Cu, Co, and Ni in core C-1, Mn, Co, and Ni in core C-2 and of Cu, Co, and Ni in core C-3. Mn was severely to very severely contaminated in core C-3. The mean probable effect level quotient and mean effect range median quotient showed medium to low-level contamination of Cu, Ni, and Zn. Metals were considerably allied to Fe-Mn oxide and organic/sulphide fractions which revealed their bioavailability. Mn was 36% in labile form (lower estuary) and indicated a high risk to biota. Mn, Ni, and Zn in Saccostrea cucullata exceeded the permissible limit and suggested toxicity and non-suitability for human consumption.