Microplastics (MPs) have become an emerging global pollutant due to their widespread dispersion and potential threats to marine ecosystems. However, studies on MPs in estuarine and coastal ecosystems of Bangladesh are very limited. Here, we conducted the first study on abundance, distribution, characteristics, and risk assessment of microplastics in the sediment of Karnaphuli River estuary, Bangladesh. Microplastic particles were extracted from sediments of 30 stations along the estuary by density separation and then enumerated and characterized using a stereomicroscope and Fourier Transform Infrared (FT-IR) spectroscopy. In the collected sediment of the Karnaphuli River estuary, the number of MPs varied from 22.29 to 59.5 items kg−1 of dry weight. The mean abundance was higher in the downstream and left banks of the estuary, whereas the predominant shape, colour, and size of MPs were films (35%), and white (19%), and 1–5 mm (30.38%), respectively. Major polymer types were polyethylene terephthalate, polystyrene, polyethylene, cellulose, and nylon. MPs were found to pose risks (low to high) in the sediment of the estuary, with the highest risk occurring at one station near a sewage outlet, according to the results of risk analyses using the pollution risk index, polymer risk index (H), contamination factors, and pollution load index (PLI). The single value index, PLI, clearly demonstrated that all sampling sites were considerably polluted with microplastics (PLI > 1). H values showed toxic polymers, even in lower proportions, possess higher polymeric hazard scores and vice versa. This investigation uncovered new insights on the status of MPs in the sediments of the Karnaphuli River estuary, laying the groundwork for future research and control of microplastic pollution and management.