Microplastic (MP) pollution is a major global issue that poses serious threats to aquatic organisms. Although research on MP pollution has been extensive, the relationship between MPs and water quality parameters in estuarine water systems is unclear. This work studied the spatiotemporal distribution and characteristics of MPs in the Karnaphuli River estuary, Bangladesh. MP abundance was calculated by towing with a plankton net (300 μm mesh size) at three river gradients (up-, mid- and downstream) and the association between physicochemical parameters of water (temperature, pH, salinity, electrical conductivity, total dissolved solids, and dissolved oxygen) and MP distribution patterns was also investigated. Mean MP abundance in water was higher during the wet season (April) (4.33 ± 2.45 items per m3) compared to the dry season (September) (3.65 ± 2.54 items per m3). In descending order, the highest MP abundance was observed downstream (6.60 items per m3) > midstream (3.15 items per m3) > upstream (2.22 items per m3). pH during the wet season (April) and temperature during the dry season (September) were key physicochemical parameters that correlated with river MP abundance (r = −0.74 and 0.74 respectively). Indicating that if the Karnaphuli River water has low pH or high temperature, there is likely to be high MPs present in the water. Most MP particles were film-shaped, white in color, and 1–5 mm in size. Of the six polymers detected, polypropylene (PP), polystyrene (PS), polyethylene terephthalate (PET), and cellulose were predominant, comprising roughly 17–19% each. These results can be used to model MP transport in the freshwater ecosystem of the Karnaphuli River estuary in Bangladesh to help develop future mitigation strategies.