The fate of antibiotic resistance genes (ARGs) in aquatic environments, especially in rivers and reservoirs, is receiving growing attention in South Korea because reservoirs are an important source of drinking water in this country. Seasonal changes in the abundance of 11 ARGs and a mobile genetic element (int1) in two reservoirs in South Korea, located near drinking water treatment plants in Cheonan and Cheongju cities, were monitored for 6 mo. In these drinking water sources, total ARG concentrations reached 2.5 × 107 copies mL‒1, which is one order of magnitude higher than in influents of some wastewater treatment plants in South Korea. During the sampling periods in August, October, and November 2016 and January 2017, sulfonamides (sul1), β‐lactam antibiotics (blaTEM), and tetracycline (tetA) resistance genes were the most abundant genes at the two sites. The ARG abundance consistently increased in January relative to 16S ribosomal ribonucleic acid (rRNA) counts. General stress responses to oxidative stress and other environmental factors associated with the cold season could be significant drivers of ARG horizontal gene transfer in the environment. Accordingly, removal of ARGs as a key step in water treatment warrants more attention. Core Ideas Total ARG concentrations were alarmingly high in fresh water drinking water sources in South Korea. Most ARGs conferred resistance to sulfonamides, β‐lactam antibiotics, and tetracycline. ARG growth and transport from nonpoint sources may be significant in antibiotic resistant bacteria fate in summer. Horizontal gene transfer could be a more important factor in ARG amplification in winter. The role of water treatment plants in the removal of ARGs should be emphasized.