Dissemination of antibiotic resistance genes (ARGs) in the water environment has become an increasing concern. There have been many reports on ARGs in surface water, but little is known about ARGs in groundwater. In this study, we investigated the profiles and abundance of ARGs in groundwater in comparison with those in surface water of Maozhou River using high-throughput quantitative PCR (HT-qPCR). Totally 127 ARGs and 10 MGEs were detected by HT-qPCR, and among them the sulfonamides, multidrug and aminoglycosides resistance genes were the dominant ARG types. According to the results of HT-qPCR, 18 frequently detected ARGs conferring resistance to 6 classes of antibiotics and 3 MGEs were further quantified by qPCR in the wet season and dry season. The absolute abundance ranged from 1.23 × 105 to 8.89 × 106 copies/mL in wet season and from 8.50 × 102 to 2.65 × 106 copies/mL in the dry season, with sul1 and sul2 being the most abundant ARGs. The absolute abundance of ARGs and MGEs has no significant difference between the wet season and dry season while the diversity of ARGs in the dry season was higher than that in the wet season (p < 0.05). Totally 141 and 150 ARGs were detected in the water and sediments of Maozhou River, respectively. A total of 116 ARGs were shared among the groundwater, river water, and sediment, which accounted for 67.1% of all detected genes. Redundancy analysis further demonstrated that the environmental factors contributed 70.7% of the total ARG variations. The findings of large shared ARGs, abundant Total Coliforms and large wastewater burden in the groundwater provide a clear evidence that anthropogenic activities had a significant impact on groundwater.