Microplastic (MP) pollution has reached the remotest areas of the globe, including the polar regions. In the Arctic Ocean, MPs have been detected in ice, snow, water, sediment, and biota, but their temporal dynamics remain poorly understood. To better understand the transport pathways and drivers of MP pollution in this fragile environment, this study aims to assess MPs (≥ 11 μm) in sediment trap samples collected at the HAUSGARTEN observatory (Fram Strait) from September 2019 to July 2021. MP fluxes determined by μ-Fourier transform infrared (FTIR) imaging ranged from 0 to 2.9 MP m−2 d−1, peaking in April 2020 and April 2021, with all detected MPs being <300 μm in size. There was no strong correlation between MPs and any of the recorded biogeochemical and physical variables, as each MP flux event was associated with different variables such as biogenic matter, sea ice concentration, or origin. By providing time series data over 21 months, this study provides a baseline for future MP flux assessments in Fram Strait, Arctic.