In this paper, water and sediments were sampled at eight monitoring stations in the coastal areas of the Yangtze
River Estuary in summer and autumn 2021. Two sulfonamide resistance genes (sul1 and sul2), six tetracycline
resistance genes (tetM, tetC, tetX, tetA, tetO, and tetQ), one integrase gene (intI1), 16 S rRNA genes, and microbial
communities were examined and analyzed. Most resistance genes showed relatively higher abundance in summer
and lower abundance in autumn. One-way analysis of variance (ANOVA) showed significant seasonal variation
of some ARGs (7 ARGs in water and 6 ARGs in sediment). River runoff and WWTPs are proven to be the major
sources of resistance genes along the Yangtze River Estuary. Significant and positive correlations between intI1
and other ARGs were found in water samples (P < 0.05), implying that intI1 may influence the spread and
propagation of resistance genes in aquatic environments. Proteobacteria was the dominant phylum along the
Yangtze River Estuary, with an average proportion of 41.7%. Redundancy analysis indicated that the ARGs were
greatly affected by temperature, dissolved oxygen, and pH in estuarine environments. Network analysis showed
that Proteobacteria and Cyanobacteria were the potential host phyla for ARGs in the coastal areas of the Yangtze
River Estuary.