Microplastics are small plastic fragments less than 5 mm in diameter, and microplastic pollution is an emerging threat in our day to day life. Microplastic pollution was estimated in water, sediment and fish samples from selected stations along the Cochin estuary and nearby coastal areas in Kochi. The estuarine water and sediment samples recorded a larger number of microplastics than in beach samples with a mean abundance of 751.7 ± 452.21 particles/m3 and 1340 ± 575.22 particles/kg, respectively. Study stations near to the busiest city locations showed significantly high levels of microplastic pollution (p < 0.001). A total number of 46 fishes belonging to five species were dissected, from which nine microplastics were isolated. All of the isolated plastic materials were identified as secondary microplastics. Among different types, fibres were abundant in all the sampling sites. Selected particles were identified with Fourier Transform Infrared Spectroscopy analysis as cellophane, polystyrene, polyethylene, polypropylene, and nylon. The study found that the water and sediment samples from the Cochin estuary are seriously polluted with microplastics, and this is the first attempt to compare the microplastic pollution status of the Cochin estuary with the associated beaches.