As emerging environmental contaminants, ensuring the security of water supplies requires a critical understanding of the occurrence, transmission mechanisms and risk control of antibiotic resistance genes (ARGs) in basin water environments. This paper provides a systematic review of the characteristics of the occurrence, pollution sources and spatiotemporal distribution patterns of ARGs in China’s seven major river basins: the Yangtze, Yellow, Huaihe, Pearl, Haihe, Liaohe and Songhua rivers. The paper also analyses the migration and diffusion mechanisms of ARGs in combination with the effects of combined pollution from eutrophication, heavy metals, and emerging contaminants (e.g., antibiotics, microplastics, endocrine-disrupting chemicals, and persistent organic pollutants). The study reveals that sulfonamides, tetracyclines, and aminoglycosides dominate ARGs in China’s basin water environments, primarily originating from non-point source pollution (e.g. agricultural planting and livestock and poultry farming) and point source emissions (e.g., wastewater treatment plant effluents and medical wastewater). In terms of occurrence levels, the absolute abundances of ARGs in sediments (10⁶-10¹⁰ copies/g) are generally three orders of magnitude higher than in water bodies (10³-10⁷ copies/mL), although their relative abundances (copies/16S rRNA) are similar. Spatiotemporally, ARGs are driven by microbial communities, environmental physicochemical factors, human activities and mobile genetic elements (MGEs), with microbial communities exerting the most significant influence. In terms of the effects of pollution, water eutrophication promotes the proliferation of bacterial communities that host ARGs, such as nitrate-reducing bacteria. This results in a significant positive correlation between ARG abundances and total nitrogen and total phosphorus loads. Heavy metals (e.g., copper, zinc and nickel) enhance the efficiency of ARG conjugative transfer through co-selection effects. Emerging contaminants such as antibiotics exert selective pressure on ARGs, while microplastic biofilms can increase ARG transformation frequencies by up to 1000-fold compared to natural substrates. Endocrine-disrupting chemicals (e.g., bisphenol A) and persistent organic pollutants (e.g. perfluorooctanoic acid) promote ARG horizontal transfer by inducing oxidative stress or upregulating plasmid expression. ARG transmission mechanisms primarily include shaping of the bacterial community (e.g., selective enrichment ofFirmicutes andProteobacteria), conjugative transfer (dependent on MGEs and ATP energy metabolism), induced transformation (extracellular DNA adsorption onto suspended particulates) and phage-mediated transfer (preferential packaging of ARG fragments). Notably, fluvial sediment dynamics processes such as suspended sediment transport and resuspension significantly influence ARG transmission fluxes by regulating pollutant partitioning across phases. Future research should investigate the coupled processes of “sediment-water dynamics-contaminants-ARGs”, analyse the cross-scale regulatory mechanisms of ARGs in multi-phase water environments and explore the potential application of sediment-water ecological regulation in ARG risk management.