Baiyangdian Lake is a typical and largest multi-habitat lake in the North plain of China. To understand the generation and transmission of antibiotics resistance genes (ARGs) in multi-habitat lakes, the contents of nutrients (TC, TOC, TN, TP and TS), heavy metals (Zn, Cr, Ni, Cu, Pb, As, Cd and Hg), 22 antibiotics, 16S-rRNA(16S), Class I integron (intI1) and 20 ARGs were determined. Samples were taken from the Fuhe river, river estuaries, reed marshes, living area, sh poods and open water of Baiyangdian Lake. The results showed that quinolones (QNs) were the main pollutants, and the content range was ND-104.94 ng/g. Thereinto, aac (6') -IB, blaTEM-1, ermF, qnrA, qnrD, tetG, sul1, sul2 and tetM were detected in 100%. The absolute abundance of sul1 was the highest (5.25×10 5 copies/g-6.21×10 7 copies/g), which was the dominant ARGs. In these different habitats, the abundance of antibiotics and ARGs in river estuary was the highest, and that in reed marshes was the lowest. There was a signi cant positive correlation between the abundance of heavy metals (Cu, Pb, Zn, Ni, Cd, Hg) and the absolute abundance of 11 ARGs (P<0.01). Redundancy analysis showed that Cu, Zn, intI1, TP and macrolides (MLs) were the important factors affecting the distribution of ARGs. Our ndings provides a more likely driving and in uencing factor for the transmission of ARGs in lakes with complex and diverse habitats.