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, fish ponds and open water of Baiyangdian Lake. The results showed that quinolones were the main pollutants in six habitats, and the content range was ND-104.94ng/g. Thereinto, aac (6') -IB, blaTEM-1, ermF, qnrA, qnrD, tetG, sul1, sul2 and tetM were detected in all the analyzed samples. The absolute abundance of sul1 was the highest (5.25 × 105 copies/g-6.21 × 107 copies/g) in most of the samples. 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 significant 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 were the important factors affecting the distribution of ARGs. Our finding provides a more likely driving and influencing factor for the transmission of ARGs in lakes with complex and diverse habitats.