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Microplastic (MP) pollution is widely spread in oceans, freshwater, and terrestrial environments but MPs in mountainous headwater ecosystem are rarely reported. This study focuses on the headwater of Yangtze tributaries of the Hindu Kush-Himalayan (HKH) region. Five streams at elevations of 900 to 3300 m were selected to investigate the distribution of MPs in water and sediments across altitudes. MPs were found in all water and sediment samples from top stream zone nearly in absence of anthropogenic activity, low anthropogenic zone, and high anthropogenic zone, increased from 12–54, 81–185 to 334–847 items/L, and 2–35, 26–84 to 124–428 items/kg, respectively. This elevation-dependent MP distribution indicated that as elevation decreased, anthropogenic activities intensified and increased MPs input and their abundance, size, and diversity. Notably, hydraulic projects, such as damming, were identified as potential barriers to the migration of MPs downstream. Microbiome analyses revealed the presence of bacterial genes associated with plastic biodegradation in all sediment samples. The study indicates that Shangri-la mountainous streams have been polluted with MPs for years with potential risk of generation of nano-sized particles via natural fragmentation and biodegradation, and thus raises concern on MPs pollution in headwaters streams in mountainous regions. [Display omitted] • Anthropogenic and biological activities elevate MPs pollution in mountain headwaters. • MPs pollution observed in top and increased towards downstream. • Hydraulic projects e.g. damming prevent MPs migration to downstream. • Genes of 15 bacterial genera associated with plastic degradation was found in sediments. • MPs have symptoms of further degradation into more ecologically risky nanoplastics. [ABSTRACT FROM AUTHOR]