Abstract Microplastics (MPs) are an anthropogenic pollutant of emerging concern prominent in both raw and treated municipal wastewater as well as urban and agricultural run-off. There is a critical need for the mitigation of both point- and diffuse sources, with treatment wetlands a possible sustainable nature-based solution. In this study, the possible retention of MPs in treatment wetlands of the widely used surface flow (SF) type was investigated. In- and outflow water, as well as atmospheric deposition, at a full-scale reed-based SF wetland (operating as a polishing phase of municipal wastewater treatment) was analyzed for MPs in a size range of 25–1000 μm. FPA-based μFT-IR spectroscopic imaging was used in combination with automated data analysis software, allowing for an unbiased assessment of MP numbers, polymer types and size distribution. Inflow water samples (secondary treated wastewater) contained 104 MPs m−3 and 56 MPs m−3 in sampling campaigns 1 and 2, respectively. Passage through the SF wetland increased the MP concentration in the water by 92 % during a rain intense period (campaign 1) and by 43 % during a low precipitation period (campaign 2). The MP particle numbers, size and polymer type distribution varied between the two sampling campaigns, making conclusions around the fate of specific types of MPs in SF wetlands difficult. Atmospheric deposition was measured to be 590 MPs m−2 week−1 during the rain-intense period. Our findings point towards atmospheric deposited MPs as an important factor in the fate of MPs in SF wetlands, causing an increase of MP concentrations, and potentially explaining the variations observed in MP concentrations in wetland effluent and removal efficiency. Furthermore, atmospheric deposition might also be a reason for the considerable inter-study variation regarding MPs removal efficiency in SF wetlands found in the available literature.