As emerging environmental contaminants, antibiotic resistance genes (ARGs) and their transmission mechanisms and risk control in basin water environments represent critical scientific issues for ensuring water security. This paper systematically reviews the occurrence characteristics, pollution sources, and spatiotemporal distribution patterns of ARGs in the water environments of China’s seven major river basins (Yangtze River, Yellow River, Huaihe River, Pearl River, Haihe River, Liaohe River, and Songhua River). It also analyzes the migration and diffusion mechanisms of ARGs in combination with the combined pollution effects of eutrophication, heavy metals, and emerging contaminants (antibiotics, microplastics, endocrine-disrupting chemicals, persistent organic pollutants, etc.). The study shows that ARGs in China’s basin water environments are dominated by sulfonamides, tetracyclines, and aminoglycosides, primarily sourced from non-point source pollution (agricultural planting, livestock and poultry farming, etc.) and point source emissions (wastewater treatment plant effluents, medical wastewater, etc.). In terms of occurrence levels, the absolute abundances of ARGs in sediments (106~1010 copies/g) are generally three orders of magnitude higher than those in water bodies (103~107 copies/mL), though 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. Regarding pollution effects, water eutrophication promotes the proliferation of ARG-hosting bacterial communities such as nitrate-reducing bacteria, resulting in a significant positive correlation between ARG abundances and total nitrogen (TN) and total phosphorus (TP) loads. Heavy metals (e.g., Cu, Zn, Ni) enhance ARG conjugative transfer efficiency through co-selection effects. Among emerging contaminants, antibiotics drive ARG evolution through selective pressure; microplastic biofilms can increase ARG transformation frequencies to 1,000 times those of natural substrates; and 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 bacterial community shaping (e.g., selective enrichment of Firmicutes and Proteobacteria), conjugative transfer (dependent on MGEs and ATP energy metabolism), induced transformation (extracellular eDNA adsorption onto suspended particulates), and phage-mediated transfer (preferential packaging of ARG fragments). Notably, fluvial sediment dynamics processes, such as suspended sediment transport and sediment 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," analyze cross-scale regulatory mechanisms of ARGs in multi-phase water environments, and explore the application potential of sediment-water ecological regulation in ARG risk management.