Industrial aquaculture relies on antibiotics such as florfenicol to combat disease and maintain production, but microbial risks, particularly concerning antibiotic resistance genes (ARGs) after the mandated withdrawal time, are poorly understood. To address this, we simulated standard and prolonged florfenicol treatments in common carp (Cyprinus carpio) and performed metagenomic analyses of the gut resistome, mobilome and microbiome. Here we show that florfenicol administration caused significant resistome shifts. While ARG abundance decreased during post-treatment times, it remained elevated above control levels even after the mandated withdrawal time. Integrons and a composite transposon harbouring floR facilitated ARG dissemination during florfenicol treatments. Following withdrawal, gut microbiota of fish subjected to prolonged treatments harboured more diverse ARG-carrying plasmids than controls. Although the dominant microbiota showed resilience, some ARG-carrying bacteria remained enriched. Of the enriched potential pathogens, 47.1% harboured ARGs identical to those on plasmids. Crucially, the high similarity between plasmid and chromosomal ARG-flanking sequences underscores a key role of plasmid in ARG transfer. Overall, florfenicol treatment increased both the abundance and the mobility of ARGs in the carp gut. The resistome and mobilome profiles did not return to baseline after the mandated withdrawal time, indicating that this period is insufficient to mitigate the ARG transmission risk.