The dataset provides information about the microplastic contamination in subsurface water samples pumped from a depth of ∼11.2 m in the Weddell Sea, Antarctica. Samples (n = 79) were collected between the latitudes 52°S and 71°S, during expedition PS117 (2018/2019) on RV Polarstern. Samples were collected continuously for 37 days with an on-board seawater intake (Klaus Union Sealex Centrifugal Pump, stainless steel, and PTFE; Bochum, Germany) delivering the subsurface seawater to the laboratory through a PTFE-coated pipe system. The seawater was filtered through stainless steel geological sieves with a 300 μm mesh. Sample sieves were recovered every 12 h, resulting in an average of 3.91 (±1.09 SD) m³ filtered seawater per sample and a total of 304 m³. One subsurface water sample was taken parallel to the discharge outlet of the ballast water of the research vessel (filtered vol.: 0.77 m³, vol. of discharged ballast water: ∼250 m³). Putative microplastic particles were sorted visually under a dissecting microscope (magnification 6.7-45x) and analyzed by means of by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy.