Water bodies in hilly areas are considered the cleanest in India. They are also sites for household and recreation activities. On the contrary, they are disposal sites for household and toxic industrial wastes. This study evaluates the physio-chemical parameters and the toxic heavy metal content in two water bodies of Itanagar, the capital city of the Himalayan state of Arunachal Pradesh. Physiochemical parameters were evaluated using standard procedures and toxic heavy metal contents were analyzed using Inductively coupled plasma optical emission spectroscopy. The study revealed high dissolved oxygen contents in both water bodies. Other parameters such as alkalinity, carbon dioxide, phosphate, chloride, and nitrate contents were found to be within the permissible limits. However, lead and arsenic were found in trace amounts but below the permissible limits in both water bodies. Cadmium was exactly within the permissible limit whereas, antimony was found to exceed the permissible limit (0.010ppm). Also, chromium (0.070±0.002 ppm) in Ganga Lake and nickel (0.086±0.011 ppm) in Poma River were found to be above the permissible limits. The presence of toxic metals in these natural hilly areas is alarming and can be attributed to increasing anthropogenic activities. Adequate measures and precautions to prevent such contamination activities should be undertaken.