Trace metals are a group of toxic pollutants that can cause serious damage to ecosystems and humans. To determine the distribution characteristics of aqueous trace metal contamination and identify critical pollution sources, it is necessary to develop a detailed estimation of trace metal emissions. By considering emission-related factors in each industrial sector, we estimate that the emissions were approximately 2, 61 t, 2,684 t, 301 t and 309 t for mercury, cadmium, chromium, arsenic and lead, respectively, in 2010 in China. These values are much higher than those provided in annual statistical reports. Our research identified critical emissions sources, including Shandong, Henan, Jiangsu and Guangdong Provinces and Raw Chemical, Non-ferrous Smelting, Non-ferrous Mining and Metal Products industries. However, Shandong and Metal Products are ignored in ‘The Twelfth 5-Year Plan for Complete Control of Trace Metal Pollution’. This research generally found that the allowable discharge levels had a significant impact on specific sectors. Total emissions are much lower than the maximum allowable under current Chinese emissions regulations but exceed limits recommended by Integrated Pollution Prevention and Control (European Union). Furthermore, our study found that many regions located along upstream reaches of the Yangtze River, like Sichuan Province, are sources of cross-boundary pollution.