Due to economic development and population growth, the water shortage in China has gradually become increasingly severe. In this paper, by developing an environmentally expanded input-output (IO) model, water footprint in China during 2002–2012 is calculated from the perspective of final demand. Furthermore, a structural decomposition analysis (SDA) model is used to study the driving factors of the water footprint of rural and urban household consumption, gross fixed capital formation and exports. The findings indicate that: 1) the water footprint driven by final demand in China increased by 18.3% during 2002–2012, reaching 617.68 billion m3 in 2012, of which urban household consumption accounts for the highest proportion. 2) Of the different sectors, agricultural commodities have the highest water footprint, accounting for 35% of national water footprint in 2012. 3) In terms of the driving factors, water efficiency inhibits the increase of water footprint regardless of final demand types, while GDP per capita makes a great contribution to its rise. 4) As for rural household consumption, the most important driving factor is the inhibition effects of consumption pattern in water footprint. For urban household consumption, the water footprint is inhibited by consumption pattern but promoted by production structure during 2002–2010. However, it is no longer the case during 2010–2012 that consumption pattern becomes a promoting factor, with production structure being inhibiting one. 5) Regarding gross fixed capital formation, its water footprint increase driven by consumption pattern is only 12.4 billion m3 during 2007–2010. As for exports, consumption pattern causes the decline of water footprint after 2005 and the overall water footprint of exports declines during 2007–2012. Finally, this paper provides policy implications with respect to the promotion of China’s water footprint conservation.