Improper disposal of domestic sewage and effluents from drug manufacturing units for several years has resulted in the accumulation of pollutants in Musi river sediments. There were no studies carried out before to quantify the antibiotic resistance in this river, despite the fact that its sediments are loaded with antibiotics. The present study investigated the relationship between the proliferation of ciprofloxacin resistant culture with the occurrence of fluoroquinolone and heavy metals in sediments of Musi River. The fluoroquinolones concentration in river sediments were observed in high concentration (13336.4 ng/g) and were found to be positively correlated with the occurrence of ciprofloxacin resistant bacteria (r = 0.386 to 0.675, p < 0.05). The occurrence of heavy metals was also in positive correlation with the distribution of antibiotic resistant bacteria in the river (r = 0.454 to 0.881, p < 0.05). This study indicated the spread of antibiotic resistance in polluted river sediments that might pose a serious threat to public health as the river water is used for irrigation, drinking, and recreational purposes; and needs an immediate risk assessment and mitigation strategies. © 2017 Taylor & Francis Group, LLC.