Metals are non-degradable in the aquatic environment and play a vital role in estuarine biogeochemistry but could also be detrimental to associated biota. A comparative evaluation of the trace metal concentrations (Fe, Mn, Zn, Cu, Ni, and Co) was carried out in the Zuari estuary, Goa during the post-monsoon season of 2013 at six locations, each representing three mangrove and three mudflat regions. In addition, fractionation of trace metals in sediments was performed to provide information on the mobility, distribution, bioavailability and toxicity. Special attention was paid to the marine mollusks viz. bivalves and gastropods that are extensively used as bio-indicators in coastal pollution. Considering the percentage of metals in the sequentially extracted fractions, the order of mobility from most to least bioavailable forms was Mn >Zn >Cu >Ni >Co >Fe. Mn maintained high bioavailability (average around 60%) in Fe-Mn oxide and carbonate bound forms indicating that Mn is readily available for biota uptake. The bioavailability of Fe was on an average of around 6% whereas other metals like Cu, Zn, Ni and Co were around 19% to 34%. When the bioavailable values were compared with standard Screening Quick Reference Table (SQUIRT), Zn showed higher toxicity level and bioavailability in the lower estuary. On the basis of calculated Bio Sediment Accumulation Factors (BSAF's), overall trend in bioaccumulation was in the order of Cu >Zn >Mn >Ni >Co >Fe. Metal Pollution Index (MPI) computed was higher for gastropods than bivalves.