Mangroves and mudflats, important sub environments within the estuaries, are rich in nutrients and are potential sources for flora and fauna and thus provide shelter to thousands of animal and plant species. The sediments in these sub-environments composed of different geochemical phases that act as potential binding sites for metals. The metals are present in various forms and metal bioavailability includes metal species that are bio-accessible. A modified sequential extraction procedure, screening quick reference table, sediment quality guidelines as standard approaches are available to quantify different forms of metals. Our investigation revealed that Mn values are above Apparent effects Threshold (AET), indicating Mn is bioavailable and toxic to biota in mudflats of many estuaries in India. Among the trace metals Co and Zn show higher bioavailability. Distribution pattern of bioavailable metals can also be used to understand anthropogenic input to the estuaries and their mobilization.