China has implemented strict policies for the installation of desulfurization facilities in coal power plants in order to mitigate their negative environmental and human health impacts. However, it is rarely acknowledged that desulfurization processes lead to increased water consumption and carbon emissions from the coal power sector. By using a bottom-up approach, we quantified that the desulfurization facilities in all of China’s coal power plants together avoided emissions of 29.52 Mt of SO2 in 2014, with expenses of 550.26 million m3 of increased water consumption, and 53.28 Mt of additional CO2 emissions. Such conflicts were especially pronounced in the North China Grid, where 9.77 Mt of SO2 emission reductions were realized at expenses of 132.15 million m3 of water consumption, and 14.25 Mt of CO2 emissions. The provinces in the North China Grid were already facing extreme water scarcity. Furthermore, while more than 90% of China’s coal power plants have installed desulfurization facilities, the application of full desulfurization would further reduce the greatest amount of SO2 emissions with the smallest amounts of additional water consumption and carbon emissions in the Northwest Grid. Replacing all wet desulfurization facilities with dry ones saves 498.38 million m3 of water consumption in total, and reduces 26.65 Mt of CO2 emissions; however, this is at an expense of 14.33 Mt of SO2 emissions. These conflicts are most pronounced in Shanxi Province in the North Grid, and in Guangdong Province in the South Grid.