Antimicrobial resistance (AMR) is a silent pandemic, rising sharply worldwide and having particularly severe impacts in low- and middle-income countries (LMICs). This is largely driven by rapid urbanization and the lack of adequate wastewater treatment infrastructure, resulting in the direct discharge of untreated wastewater into urban rivers and thereby contributing to the spread of AMR. However, the extent, fate, transport, and ecotoxicological implications of AMR pollution in these urban environments remain scarce. This study quantified taxonomic and antibiotic resistance genes (ARGs), resistant and sensitive bacteria, and environmental conditions in the Musi River that runs through Hyderabad, a city containing the largest manufacturers of pharmaceutical products. Furthermore, a total of 25-point sources were identified, wastewater inputs were estimated, and a hydraulic model was developed to study the rapid fluctuations in river flow and pollution concentrations along the river stretch passing through the city. The ecotoxic effects of polluted river water on zebrafish larvae were also assessed. Our findings revealed increasing, though spatially variable, concentrations in ARGs along the river through the dry season, and stronger discrete point source and flow dilution dynamics in the wet season. The riverbed sediment stores far higher concentrations of ARGs than the water column, especially in the dry season, and has more dynamic interaction with the river during the wet season. The river modeling indicated that approximately 60% of the flow in the city stretch comprises untreated wastewater. Moreover, the observed lethal and sub-lethal ecotoxic effects on zebrafish larvae underscore the environmental and biological risks associated with sewage pollution. This study highlightsthe urgent need for expanding wastewater treatment capacity to reduce raw discharges and mitigate AMR risks, an issue of growing concern across the urban rivers of LMICs.