Antibiotics and antibiotic resistance genes (ARGs), as emerging environmental pollutants, are ubiquitous in various environments, affecting microbial community structure and threatening human health, and have become a global concern. In this study, five representative large yellow crock-breeding bases in Zhejiang Province were selected as the research objects. By using ultra-high performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS), 16S rRNA high-throughput sequencing, isolation and purification, metagenomic sequencing and other technologies, the pollution levels of antibiotics were respectively detected, and the microbial diversity in seawater and sediments was compared and analyzed. The drug-resistant strains in culture environment were isolated and identified, and the pollution characteristics of ARGs in sediments were preliminarily explored. In addition, the risk of antibiotic occurrence was evaluated by means of risk entropy method, the distribution of pathogenic bacteria and probiotics was predicted by Bugbase phenotype prediction, the resistance characteristics of drug-resistant bacteria were analyzed based on drug sensitivity test, and the potential influencing factors of ARGs transmission were identified by network analysis and redundancy analysis.