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Spatial uptake patterns of microplastics (MP) by marine species are largely unexplored under field conditions. A novel “biodeposit trap” that measure uptake and egestion of MP by suspension-feeders through the analysis of their biodeposits, was designed and used to estimate the spatial variation of these processes by mussels in field conditions. Traps containing wild or farmed mussels or control empty shells were deployed at three sites characterised by different MP concentrations and water flow conditions. A different MP dimensional composition was observed between MP pools present in biodeposit and control traps, with the latter shifted towards higher dimensional range (0.05–5 mm). Conversely, mussels accumulated small MP (0.02–0.05 mm) into their biodeposits without any significant difference between wild and farmed specimens. MP uptake rates were on average 4–5 times higher at the site where MP contamination was expected to be highest and where water flow conditions were considered moderate.