The number of studies on microplastic accumulation in marine organisms has increased precipitously recently, though information is geographically-skewed and limited in terms of local effects. We characterized microplastic accumulation in oysters (Saccostrea cucullata) along a Bornean coastline, focusing on spatial variation. Comparisons were made between locally-polluted (Brunei Estuarine System, BES) and relatively pristine, open-shore (South China Sea, SCS) coastlines. Sixteen coloured microplastic types were characterized into three shapes (fragments, fibres, pellets). Fragments (74.9%), especially smaller polypropylene black fragments predominated in the samples (<50 μm, 31.7%). Site-specific levels of microplastic accumulation varied from 0.43 to 7.20 particles/g oyster tissue. BES and SCS sites differed qualitatively, indicating limited interaction. In the BES, accumulation was greatest near the predicted source (Bandar) and declined strongly seawards, implying current flow, environmental sequestration (local sinks) and seawater dilution effects. Such local-scale variation in microplastic loading in estuaries cautions against extrapolating from limited sampling.