Grain size, total organic carbon, total metals and their speciation was investigated in sediments from lower Chapora Estuary, middle Zuari Estuary and Moira River in Goa, India. Study aims to understand metal bioavailability and bioaccumulation in two edible bivalves (Cassosstrea spp. and Polymesoda spp.) in three water bodies of different lengths, catchment areas, hydrodynamics and anthropogenic stress. Hydrodynamics regulated coarser sediment transport and deposition at Chapora and Moira stations, while clay particles deposition at the Zuari Estuary. Considerable difference in total metal level (Mn and/or Zn) from November to December was attributed to their additional input and variation in physicochemical processes. Contamination factor revealed moderate contamination of Zn at Chapora (November), while Zn, Cu and Co were moderately contaminated at Zuari. Presence of metals in considerable or significant amount in bioavailable fractions indicated their bioavailability. Variation in metal accumulation in gills, adductor muscle and digestive gland at three stations and between months was the result of varying hydrodynamics, trophic levels, feeding habits and pollution gradients of metal causes. Interlinkage of metals in water, sediments and bivalves revealed discrepancies in accumulation of metal type. This might be attributed to differential response of species to varying physical and biological factors at study sites. Bivalves showed a selective preference for Zn at three stations highlighting its importance in biological activities. Moreover, metals in bivalves at one or more stations exceeded the standard permissible limit and thus, indicated their toxicity to bivalves and non-suitability for human consumption according to marine pollution index.