Freshwater environments are important reservoirs of antimicrobial resistance genes. However the complete resistome and associated mobilome in these ecosystems, as well as hosts of ARG in these systems are frequently missed by traditional monitoring techniques. The resistome, mobilome, and microbiome of three river systems in the Eastern Cape, South Africa, are examined in this study using shotgun metagenomic sequencing from 2021 to 2023. A wide range of antimicrobial resistance genes (ARGs) that confer resistance to several clinically significant antibiotic classes, such as aminoglycosides, beta-lactams, cephalosporins, chloramphenicol, macrolides, lincosamides, quinolones, trimethoprim, sulfonamides, tetracyclines, and streptothricin N-acetyltransferase, are identified by analysing genomic DNA from river water samples. The possible dangers posed by these aquatic habitats were further highlighted by the association of ARG-carrying reads with known pathogenic bacterial species. With its crucial understanding of both common and divergent riverine antimicrobial resistant risk across geographic patterns, this study highlights the value of metagenomic techniques in tracking AMR in freshwater systems.