Antibiotic resistance genes (ARGs) are prevalent in livestock environments. Currently, groundwater-borne ARGs in livestock farms are a growing concern as they can engender plausible risks to human health through direct drinking or indirect cross-media transmission. However, the source tracking of groundwater-borne ARGs in animal farms remains vague. In this study, the paired samples including groundwater, swine feces, wastewater, and soil from working and abandoned swine feedlots were collected and subjected to metagenomic analysis. Results showed that a total of 515 and 314 ARG subtypes, comprising some high-concerned ARGs such as aph(6)-I and aph(3’)-I, were identified in working and abandoned swine feedlots, respectively. Metagenomic assembly analysis revealed 40 ARGs, primarily conferring resistance to aminoglycoside, sulfonamide, and tetracycline antibiotics, might be transferred from aboveground sources (soil, swine wastewater, and swine feces) to groundwater mainly though plasmid-mediated horizontal gene transfer (HGT). The source tracking showed wastewater was the primary source of ARGs in groundwater. Furthermore, the culture-based approach suggested the full-length nucleotide sequences of sul1, tetA, and TEM-1 detected in groundwater-borne antibiotic-resistant bacteria (ARB) had close evolutionary relationships with those carried by same or different microorganisms from aboveground sources, reaffirming their possible spread via ARB migration and HGT. Notably, metagenomic assembly and binning analysis demonstrated that groundwater-borne ARGs were dominantly carried by human-pathogenic bacteria, especially their carried high-concerned ARGs aph(6)-I and aph(3’)-I might pose risks to human health after entering bodies via various pathways. Overall, this study highlights the transmission of ARGs from aboveground sources to groundwater in livestock farms and the potential risks associated with groundwater-borne ARGs, and provides theoretical support for advancing the precise prevention and control of ARG contamination in groundwater of animal farms.