Sundarbans, a Ramsar site of India is contaminated with heterogeneous microplastic wastes. Boddart's goggle eye mudskipper and Rubicundus eelgoby, were common gobies of Sundarbans estuary which accumulated microplastics during their normal biological activities. We estimated the abundance of microplastics in water, sediment; skin, gills, bucco-opercular cavity and gastrointestinal tract of these two goby fishes. Microplastic load estimated in gobies were 0.84 and 2.62 particles per fish species with a dominance of transparent, fibrous microplastics with 100–300 μm in length. ATR-FTIR and Raman spectroscopy revealed polyethylene as prevalent polymer. Surface degradations and adsorption of contaminants on microplastic surface were investigated by SEM-EDX analysis. Presence of hazardous polymers influenced high polymer hazard index and potential ecological risk index which indicated acute environmental threat to Sundarbans estuary and its resident organisms. Current study will provide a new information base on the abundance of microplastics and its ecological hazard in this biosphere reserve.