The giant panda (Ailuropoda melanoleuca) is recognized worldwide as an icon for wildlife conservation. The Qinling subspecies (Ailuropoda melanoleuca qinlingensis) inhabiting the Qinling Mountains is more endangered. Previous studies have indicated that Qinling pandas are potentially at risk from environmental pollutants, which they are exposed to via food and drinking water. However, there is little information about the surface water quality in the Qinling Mountains, and it is unknown whether drinking water is an important pollutant source for pandas. Water samples were collected from five different nature reserves in Qinling, each of which is home to a population of pandas. The samples were analyzed for five essential metals of copper (Cu), zinc (Zn), manganese (Mn), chromium (Cr), and nickel (Ni) and four non-essential metals of lead (Pb), cadmium (Cd), arsenic (As), and mercury (Hg). The concentrations of all heavy metals (HMs) were higher in buffer zones than in the core areas and were highest in Foping and Niuweihe nature reserves. The concentrations of mercury exceeded the water quality standard in the core zone of three reserves, suggesting that NWH (Niuweihe), THS (Tianhuashan), and PHL (Pingheliang) giant panda populations were at risk from mercury toxicity. The accumulation of other elements over time could also pose a serious risk to pandas. Three main sources of pollution were identified: coal combustion, waste incineration, and fertilizer use; traffic-related activities; and metal mining. Environmental pollution is compromising the efforts to conserve the giant panda, and measures need to be put in place to control pollution sources.