This study aims to assess the status of microplastic (MP) pollution in Lake Van (Türkiye), a vital freshwater ecosystem with a unique ecological significance. The objectives were to determine MP abundance, size distribution, type and polymer composition, and potential ecological risks to fish species. Comprehensive sampling was conducted at eight stations for water, while three of these stations specifically focused on the gastrointestinal tracts of fish. The findings indicate a high prevalence of MPs, particularly in areas with significant human activity, such as station 1 at Sapur (mean ± SD 69.08 ± 22.3 MP/m3) and station 6 at Gevaş (72.41 ± 26.9 MP/m3). Fibers were dominant in both water and fish samples, with polyethylene terephthalate (PET) and polyacrylonitrile (PAN) being the most commonly identified polymers. This study highlights the occurrence of MPs in endemic and/or economically important fish species such as tarek (Alburnus tarichi) (mean 1.50–2.25 MP/indiv.), Van loach (Oxynoemacheilus ercisianus) (mean 0.55 MP/indiv.), lizard barbel (Barbus lacerta) (mean 0.57 MP/indiv.), and Levantine scraper (Capoeta damascina) (mean 1.00–1.75 MP/indiv.). These findings highlight the potential ecological risks posed by MP contamination for ecosystem, fish, and human health, and the urgent need for targeted mitigation strategies to reduce MP pollution. The study provides critical baseline data for understanding MP dynamics in Lake Van and contributes to the broader understanding of freshwater MP contamination on a global scale.