China's water transport sector has experienced a rapid growth over recent years. In this study, we estimated the CO2 emissions from China's inland waterway, coastal and ocean freight shipping for the period of 2006 to 2012. In order to make sure that existing data can be effectively utilised and data uncertainty can be addressed, we employed three approaches to estimate CO2 emissions, including freight turnover volume‐based approach, engine operation‐based approach, and vessel activity‐based approach, respectively. Research outcomes show that CO2 emissions from China's freight shipping increased from 58.7 mt (million ton) in 2006 to 83.5 mt in 2012, with an annual growth rate of 6.1%. Currently, CO2 emissions from freight shipping accounted for around 12% of CO2 emissions from transport sector and 1% of the overall CO2 emissions in China. From the subsector perspective, ocean freight shipping contributed the most to the total CO2 emissions, with a percentage of 48.2% in 2012. However, CO2 emissions from inland waterway and coastal freight shipping had higher growth rates and their shares might increase considerably in the long‐term. Based upon our research findings, we propose our policy suggestions on mitigating CO2 emissions from freight shipping, with a special focus on ocean freight shipping.