The purpose of the present study was to find out the sources of mercury and arsenic pollution of water in the industrial area of Peshawar, the capital of Khyber Pakhtunkhwa, Pakistan. Samples of effluents, mud, and water were collected from the target area (industrial area of Peshawar), the area of water supply source, and from the less polluted area, the Lower Dir district, as the control. Hg was determined by the cold vapor generation technique, while arsenic was determined using the electrothermal atomic absorption technique. Data of the water from the industrial area were compared with that of the source area, control area, as well as with the WHO and some international drinking water quality standards. The results show that some parameters, i.e., TDS, DO, pH, and hardness, were more than the permissible limits. Textile and glass industries were found to be the major sources of Hg and As pollution. Downstream dilution of these contaminants was also observed.