Wastewaters serve as significant reservoirs of antibiotic resistant bacteria. Despite the evidence of antimicrobial resistance in wastewaters and river water in Kathmandu, direct linkage between them is not discussed yet. This study investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing bacteria and associated resistance genes in wastewaters and river water. Out of 246 bacteria from wastewaters, 57.72% were ESBL producers and 77.64% of them were multidrug resistant (MDR). ESBL producing E. coli was dominant in municipal and hospital wastewaters (HWW) as well as in river water while K. pneumoniae in pharmaceutical wastewater. The, blaSHV and blaTEM genes were prevalent and commonly co-occurred with aac(6')-Ib-cr in K. pneumoniae isolated pharmaceutical wastewater. blaCTX-M carrying E. coli from hospital co-harbored aac(6')-Ib-cr while that from municipal influent and river with co-harbored qnrS. Whole genome sequencing data revealed the presence of diverse ARGs in bacterial isolates against multiple antibiotics. In average, an E. coli and a K. pneumoniae isolate contained 55.75±0.96 and 40.2±5.36 ARGs. Multi-locus sequence typing showed the presence of globally high-risk clones with wider host range such as E. coli ST10, and K. pneumoniae ST15 and ST307 in HWW and river indicating frequent dissemination of antimicrobial resistance in wastewater of Kathmandu. Whole genome sequence data aligned with phenotypic antibiograms and PCR detected resistance genes in selected isolates. The presence of significant plasmid replicons (IncF, IncY) and mobile genetic elements (IS903, IS26) indicate high frequency of spreading antibiotic resistance. These findings indicate burden and dissemination of antimicrobial resistance in the environment and highlight the need for effective strategies to mitigate the antibiotic resistance. Environmental implicationThe antibiotic resistant bacteria with their resistance marker genes in the environment promote the transfer and proliferation of high degree of resistance. Since this study found that potential pathogenic bacteria in wastewater and river were highly resistant phenotypes and genotypes with significant sequence types containing multiple plasmid replicons and mobile genetic elements indicating severe biological pollution in Kathmandu. These findings have three key environmental implications- 1) high risk of water borne transmission of antibiotic resistant pathogens to humans and animals posing significant public health risks, 2) possible significantly higher spread of antibiotic resistance among or between environmental and clinical pathogens, and 3) identifying critical routes of ARG dissemination and establishing dependable methods for monitoring and evaluating risks, and employing technological innovations to prevent the pollution of the environment with bacteria and genes that possess resistance to antibiotics. This study also provides clues that treatment of hospital wastewater before discharging to rivers could be a notable action to mitigate the associated risks from the environment.