Extended-spectrum β-lactamase-producing Escherichia coli are important indicators of antimicrobial resistance dissemination across human, animal, and environmental compartments. This study investigated their occurrence, concentration, genomic diversity, resistance determinants, virulence profiles, and plasmid replicons in urban and rural aquatic environments in Indonesia. Water samples were collected from the Ciliwung River across Bogor, Depok, and Jakarta; the Citarum River in West Java; the Brang Biji River in Sumbawa; groundwater wells in Depok,; and the influent and effluent of domestic and hospital wastewater treatment plants discharging into the Ciliwung River. ESBL-producing E. coli were detected at all Ciliwung River sites, seven of ten Citarum River sites, six of twenty-seven Brang Biji River sites, and three of five groundwater wells. The Ciliwung River had the highest mean concentration, at (2.1 ± 2.9) × 10⁴ CFU/100 mL, with an approximately 27-fold increase from upstream to downstream. Genomic analysis revealed a highly heterogeneous population structure, including the clinically relevant lineage ST361 and several sequence types shared between wastewater, river water, and groundwater, suggesting connectivity among these compartments. Isolates carried clinically important resistance genes, including blaCTX-M-15, blaCTX-M-55, qnrS, sul, and tetA, and virulence markers associated with uropathogenic, adherent-invasive, enterotoxigenic, and extraintestinal pathogenic E. coli. Diverse plasmid replicons, particularly IncF, IncI1-Iα, IncHI1, and Col types, indicated substantial potential for horizontal gene transfer. These findings demonstrate that Indonesian rivers, wastewater effluents, and groundwater constitute interconnected reservoirs of clinically relevant ESBL-producing E. coli. Environmental and wastewater surveillance should therefore be integrated into national One Health AMR monitoring and water-safety interventions.