Alpine meadows in the eastern Qinghai–Tibet Plateau serve as core water retention zones within China’s Three-River Source Region, while simultaneously functioning as vital grassland pastures. Livestock breeding activities impose severe disturbances on aquatic environments across this plateau area, raising concerns regarding microbial community shifts and associated environmental risks. Previous studies have explored how pastoral farming reshapes microbial assemblages within alpine meadow water bodies, yet few investigations have addressed such effects on aquatic microorganisms across an entire watershed scale. In the present study, we constructed a metagenomics dataset based on next-generation sequencing to survey spatial shifts in aquatic microbial composition and community structure along a livestock pollution gradient spanning the entire course of the Baihe River, a tributary of the upper Yellow River. Taxonomic classification revealed that domain bacteria dominated all microbial communities, with their relative abundances positively correlated with the intensity of livestock contamination. Additionally, microbial richness was markedly higher in stagnant headwater habitats than in lotic downstream reaches. The generated metagenomic dataset advances our mechanistic understanding of how livestock pollution drives spatial variations in aquatic microbial assemblages in alpine meadow waters and provides a critical baseline for environmental risk management and watershed microbial monitoring on the eastern Qinghai–Tibet Plateau.
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