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Abstract Tracing the sources of microplastics (MPs) across various environmental media is currently facing significant challenges due to their complex transportable features. In this study, we conducted a comprehensive identification of MP sources in Beijing water bodies by combining MP diversity and the conditional fragmentation model, thoroughly considering local multiple sources. The resemblance in MP community compositions implied shared or similar sources in rivers and lakes, and the sources were assorted and equivalent based on the high diversity of MPs. The conditional fragmentation model can act as a proxy of fragmentation characteristics of MPs. According to the model, suburban sewage, soils, and dry and wet deposition constituted significant sources of MPs in the rivers and lakes of Beijing. The extremely high abundance of MPs (520,000 items·m−3) in suburban sewage also confirmed it as a potential source. For MPs with different polymer types and morphologies, non-fibrous polypropylene (PP) was primarily controlled by soils, whereas the contribution of sewage sludge to fibrous polyethylene terephthalate (PET) was notable. Our study provides insights for more accurate source apportionment and contributes to a better understanding of MP fate in urban environment.