The widespread use of antibiotics has significantly contributed to the spread of antibiotic resistance genes (ARGs), which have become a major challenge to global ecological and public health. Antibiotic resistance not only proliferates in clinical settings but also persists in aquatic systems, where its residues and cross-domain spread pose a dual threat to both ecosystems and human health. ARGs spread rapidly within microbial communities through horizontal gene transfer (HGT) and vertical gene transfer (VGT). Aquatic systems are the key transmission medium. This review summarizes recent studies on the Source-Transport-Sink dynamics of ARGs in aquatic environments, along with their environmental and health risk assessments, with a particular focus on the potential ecotoxicity of ARGs transmission. It also examines the distribution characteristics of ARGs across different regions and the ecological risk assessment methods employed, highlighting the limitations of existing models when addressing the complex behaviors of ARGs. By analyzing the potential hazards of ARGs to aquatic ecosystems and public health, this article aims to provide a scientific foundation for future research and the development of public policies.