River ecosystems serve as a significant habitat and water sources for diverse organisms, including humans. An important environmental and public health concern is the increase in antibiotic-resistant bacteria (ARBs) and genes (ARGs) in aquatic ecosystems brought about by excessive pollutant flow. The research highlighted the potential implications of wastewater from treatment plants, acting as a reservoir for multidrug-resistant bacteria. The analysis of the collected Gomti and Ganga rivers water samples showed high antibiotic resistant bacteria in both the rivers. The ARBs percentages in these rivers revealed high resistance, highest with ampicillin (100%), followed by cefotaxime (96.4, 63.1%), erythromycin (52.6, 57.8%), amikacin (68.4, 50.8%), tetracycline (47.3, 54.3%), nalidixic acid (47.3, 45.6%), streptomycin (68.4, 67.2%), gentamycin (43.8, 35%), chloramphenicol (26.3, 33.3,%), neomycin (49.1, 29.8%), and ciprofloxacin (24.5, 7.01%). Further, antibiotic resistance genes in Gomti and Ganga water samples disclose distinctive patterns, including resistance to ermB (25, 40%), tetM (25, 33.3%), ampC (44.4, 40%), and cmlA1 (16.6%). The presence of ARGs in the river water shows threat of transferring these genes to native environmental bacteria. To protect the environment and public health, constant research is necessary to fully understand the extent and consequences of antibiotic resistance in these aquatic habitats.