The acquisition of blaNDM-1 gene by Gram negative bacteria has emerged as critical threat to human health as these organisms display high resistance to available antibiotics. The presence of this gene has been observed in both clinical as well as environmental settings. The present study was carried out to evaluate the prevalence of blaNDM-1 containing microorganisms in water sources. A total of 241 water samples were collected from different sites in Islamabad, Rawalpindi and areas of Khyber Pakhtunkhwa. Meropenem resistant organisms were isolated and PCR was used for the detection of the blaNDM-1 gene among the resistant isolates of all the water samples, 43 meropenem resistant bacteria were isolated among which 12 isolates were found to carry blaNDM-1 gene. The blaNDM-1 isolates were resistant to most of the antibiotics but sensitive to colistin and polymyxin B. The presence of blaNDM-1 gene harboring organisms in aquatic environment is concerning and poses public health threat.