Lake Kotokel is one of the largest lakes along the eastern shore of Lake Baikal. Increasing anthropogenic pressure combined with climate variability led to a sharp decline in its ecological condition, culminating in an outbreak of Gaff disease in 2009. Moreover, Lake Kotokel may serve as a source of pollutants to Lake Baikal due to its hydrological connection via a system of rivers. In light of these factors, ongoing research seeks to identify the drivers of ecological degradation in the lake ecosystem and provide a comprehensive assessment of its current environmental status and potential adverse processes. In this study, we report, for the first time, the occurrence of microplastic particles in the surface water and sediments of Lake Kotokel. Mean microplastic concentrations were 0.59 ± 0.25 items/m3 in water and 280 ± 162 items/kg dry weight in sediments, with corresponding average microplastic masses of 2.6 ± 1.4 μg/m3 in water and 1.33 ± 1.21 mg/kg dry weight in sediments. In surface waters, microplastic were predominantly 1–3 mm in size, whereas sediments were dominated by 0.1–1 mm particles. Fibers were the most abundant morphological form, comprising 79.5% and 82.8% of particles in water and sediments, respectively. Five polymer types were identified, with polyethylene terephthalate being the most prevalent. Based on particle abundance and polymer composition, the ecological risk of microplastic in Lake Kotokel was assessed as low to moderate.