Pearl-farming is the second most important source of income in French Polynesia. However, tropical lagoons are fragile ecosystems with regard to anthropogenic pressures like plastic pollution, which threaten marine life and the pearl oyster-related economy. Here, we investigated the spatial distribution of microplastics (MP) and concentrations in surface water (SW), water column (WC) and cultivated pearl oyster (PO) from three pearl-farming atolls with low population and tourism. Microplastics were categorized by their size class, shape, colour and polymer type identified using FTIR spectroscopy. Widespread MP contamination was observed in every study site (SW, 0.2–8.4 MP m–3; WC, 14.0–716.2 MP m–3; PO, 2.1–125.0 MP g–1 dry weight), with high contamination in the WC highlighting the need to study the vertical distribution of MP, especially as this compartment where PO are reared. A large presence of small (< 200 µm) and fragment-shaped (> 70%) MP suggests that they result from the breakdown of larger plastic debris. The most abundant polymer type was polyethylene in SW (34–39%), WC (24–32%), while in PO, polypropylene (14–20%) and polyethylene were more evenly distributed (9–21%). The most common MP identified as black-grey polyethylene and polypropylene matches the polymer and colour of ropes and collectors questioning a pearl-farming origin.