Antibiotics are used to fight diseases in humans and farm animals. Their residues, however, can enter aquatic environments and affect the resistance of non-target microbial strains, and the prevalence of antibiotic resistance genes (ARGs) potentially poses negative impacts on human health. In order to better understand how the studies of antibiotics have been conducted, we analyzed the publications on antibiotics in aquatic systems for the period of 1945–2017. We applied a bibliometric analysis method by coupling cluster analysis and network analysis. Results indicated that early research on antibiotics in water was mostly performed in America and Europe, while, in recent years, publications for the same subject were dominated by China and the USA. The majority of the articles were published in journal Chemosphere and the most representative subject categories of the seven sections were “Environmental science and ecology,” “Chemistry,” “Engineering,” “Biochemistry and molecular biology,” “Water resources,” “Agriculture,” and “Pharmacology and pharmacy.” The most studied class of antibiotics was tetracyclines in wastewater. Antibiotic resistance, ARGs, Escherichia coli, and some mechanistic studies such as adsorption, toxicity, degradation, and kinetics were common topics in this field. ARGs present a major public health concern and much attention should be directed at the problems with antibiotics in the future studies of water.