The occurrence of antibiotic resistance genes (ARGs) and resistant bacteria was quantified in 17 water samples collected across Bosten Lake, Xinjiang, China. The heterotrophic plate count method was used to detect the levels of sulfonamide- and tetracycline-resistant bacteria, which have mean concentrations of 2.50 × 105 and 4.63 × 103 CFU/mL, respectively. The resistance genes of sulfonamide (sul1, sul2) and tetracycline (tetM, tetO and tetW) were detected, and results showed that all other ARGs except the tetO gene were obtained from all samples. Four of the obtained ARGs were further quantified, and results showed that the sulfonamide resistance genes were prevalent. The relative abundance was in the range of 2.81 × 10−5 to 3.33 × 10−3 for the sul1/16s-rRNA and 1.04 × 10−5 to 3.80 × 10−3 for the sul2/16s-rRNA. For the tet genes, the relative concentrations of tetM/16s-rRNA and tetW16s-rRNA ranged from 1.18 × 10−5 to 2.46 × 10−4 and 1.58 × 10−6 to 4.19 × 10−4, respectively. The concentration divergence among ARGs may be related to the different characteristics of each gene. This study validated that Bosten Lake was affected by ARGs and resistant bacteria, thus turning the lake into an important reservoir for the transfer of ARGs and resistant bacteria.