Wastewater treatment plants (WWTPs) are the most significant barrier between anthropogenic microplastics and environmental ecosystems. The distribution and characteristics of microplastics in WWTPs remain uncertain and incompletely understood, particularly in northeastern Europe (Baltic States), where there is a lack of data on microplastic pollution and distribution. This study presents the removal efficiency and variation in characteristics of microplastics in different stages of the secondary WWTP during a 3-month sampling campaign in Lithuania. The abundance, size, shape, color, and chemical composition of microplastics in the wastewater at different treatment stages were thoroughly examined, in a size range from 20 to 1000 μm. On average, 2962 ± 25 particles/L of microplastic enter the studied WWTP. The obtained microplastic removal efficiency was 55.4% ± 3.9%, highlighting the necessity to enhance wastewater treatment strategies focusing on microplastic removal. Fragment-type microplastics smaller than 100 μm were removed from wastewater samples with the highest removal efficiency. Furthermore, our study includes recommendations to improve microplastic removal efficiency and contribute to mitigating microplastic pollution. PRACTITIONER POINTS: A large number of MPs in the size range of 20-1000 μm enter Lithuanian WWTP. Small-sized MPs within a range of 20-50 μm and 50-100 μm were removed with the highest efficiency of 54.07 ± 1.68% and 56.4 ± 2.43%, respectively. The shape and size of MPs have a major impact on the efficiency of their removal. Future research should prioritize the development of economical and energy-efficient systems, specifically designed for the removal of MPs in WWTPs.