UNLABELLED: This study investigated the prevalence and co-occurrence of antimicrobial (AMR) and metal resistance (MR) in aquatic environments with different human impacts. Metagenomes from pristine, rural and urban sites in Australia were analyzed with AMR ++ and customized binning pipelines. AMR was present in all environments, while MR was mainly in rural and urban samples. AMR gene diversity was higher in rural and urban sites, exhibiting resistance to more antibiotic classes ( IMPORTANCE: Antimicrobial resistance (AMR) and metal resistance (MR) are critical global health concerns exacerbated by anthropogenic activities. The intricate mechanism underlying the interaction among anthropogenic activities, microbial communities, and resistance remains enigmatic. We developed novel bioinformatic pipelines to unveil this interaction in three aquatic environments. Our findings demonstrate the presence of specific bacterial communities that drive AMR and MR in rural and urban environments. This study underscores the significance of proper agricultural practices, comprehensive monitoring, and management strategies to reduce anthropogenic impacts on environmental resistance.