The microplastic pollution and its effects on ecosystem in the marine environment has been well studied over the past decade. In contrast, the impact of microplastic pollution in freshwater environments was understudied, e.g., only a few studies examined the amount and distribution of microplastic in rivers, as well as the contribution of rivers to the microplastic pollution in oceans. In this study we investigated the microplastic pollution in the Tamsui River and its tributaries in northern Taiwan. We collected samples with a manta net from the Tamsui River, the Dahan River, the Keelung River and the Xindian River every two weeks over a time period of three months in 2018. Additionally, we took samples from the Xindian River during a heavy rain event in February 2019. Microplastic particles in the size range of 0.3–5 mm were visually identified. Unknown particles were identified using FTIR spectroscopy. The extracted particles were counted and classified according to their shape and color. We found microplastic of varying amounts in each of the samples, which indicates a wide spread pollution in the Tamsui River and its tributaries. The amount varies between rivers and ranges in average from 2.5 ± 1.8 particles per m³ in the Xindian River to 83.7 ± 70.8 particles per m³ in the Dahan River. Our data shows a positive correlation between precipitation and amount of microplastic particles found in the rivers. Moreover, in each river we could observe a large spatial and temporal variation of the microplastic amount between the left, middle and right sections of the stream. Due to this heterogeneous distribution of particles, we suggest that samples for microplastic analysis should be taken from multiple places across a river, as well as over a certain period to account for the heterogeneous microplastic distribution in the river water.