While global plastic production is increasing, recycling rates remain low and every year high amounts of plastic products end up as waste in the environment. A topic of increasing global concern is the distribution of microplastic (MP) in the aquatic environment. MP can be a threat to ecosystems and many organisms through entanglement or ingestion. So far various studies focused on the detection of MP in the marine environment and MP was found even in remote regions all around the globe. However little is known about transport processes and distribution of MP. Rivers are assumed to be essential pathways transporting MP from land-based sources into the world’s oceans. Understanding the dynamics of MP distribution in estuaries, which are connecting rivers to the marine environment, is a crucial component for the research on riverine transport to the marine environment. In this study the occurrence of MP in the Weser estuary was investigated with regard to MP concentration, polymer composition and size class distribution. Therefore 9 surface water samples from different locations in the estuary were taken with a pump system to analyse MPs in the size range from 10 to 500 μm. For sample preparation an enzymatic treatment was applied to remove organic matrix while preserving physical and chemical integrity of MPs. Analysis was conducted with Focal plane array detector based micro-Fourier-transform-IR spectroscopy (FPA-μFTIR) followed by an automated image analysis. Between 23.7 to 1780.7 MP items m-3 were detected with generally higher concentrations near the river mouth in Bremerhaven and lower concentrations in the open North Sea. A total of 17 different polymer types were identified with a cluster of acrylates/polyurethanes/varnish being the most abundant. 95 % of MP particles detected were below 100 μm in size. Reported MP concentrations were in the higher range of reported literature values. Comparison with other studies however was difficult due to the lack of standardised methods. Establishing a standard procedure of operation is therefore recommended to ensure comparability and replicability of MP research.