Water resources have become scarcer during the past decades due to the increases in the population and economic development in the world. Responding to the concerns about the unsustainable use of global freshwater resources, the concept of water footprint has recently been developed and applied to a wide range of researches. The water footprint of a region is defined as the volume of water, including the local water resources and virtual water imports, used for the production of the goods and services consumed by the inhabitants of the region. Water is not only consumed directly but also indirectly during the production processes. Therefore, water footprint shows the extent of water use in relation to the consumption of people in addition to traditional production-sector-based indicators of water use. The objectives of this study were to assess the water footprint of Beijing and the possible agricultural practices to reduce it. The water footprint of Beijing and characteristics of agricultural water structure were analyzed from 1990 to 2005. Three indicators, water scarcity (WS), water self-sufficiency (WSS) and water import dependency (WD) were used to evaluate the sustainability of water resources utilization. The water footprint of Beijing increased from 81.5×108 m3 in 1990 to 168.6×108 m3 in 2005, and the average water footprint per capita increased from 750.1 m3 to 1096.0 m3 during the same period. The water scarcity ratio grew from 227% in 1990 to 727% in 2005 and the water footprint of Beijing had largely been externalized by the decreasing water self-sufficiency combined with the increasing water import dependency since 1995. The average annual agricultural water use contributed to the total local water consumption by 55.1%, and the average annual net virtual water import in agricultural sector accounted for 89.1% of the gross net virtual water import. Water used for crop production was responsible for 91.9% of agricultural water use annually on average. The planting area of crops with high water consumption such as vegetables and fruits had significantly increased during the past 16 years. Correspondingly, the water consumption of these crops tremendously increased and put great pressure on the local water resources. Drinking and service water use of livestock also grew along with the expanding of animal husbandry whereas the average annual virtual water import made up 81.3% of the total virtual water of livestock production during 20012005. From the water resources point of view, livestock production might have a positive role in alleviating water scarcity of Beijing. In conclusion, water resources utilization in Beijing was unsustainable recently. As a large water user, agricultural sector had great potential to reduce the water footprint of Beijing. Strategies such as decreasing the planting area of water-intensive crops, expanding livestock production by taking advantage of virtual water import should be applied in future. In addition, as an international large city, the situation of Beijing′s ecological environment was broadly concerned. Thus, the ecological service function of farming system in Beijing should not be ignored whiles reducing water footprint. So optimizing the structure of agriculture, the limited water resources, economic, ecological and social factors must be taken into consideration together.