It is widely recognized that human activities and climate variability are two important factors that affect water resources and freshwater ecosystems. Previous evaluation work on water resources has predominantly focused on the qualification of blue water flow. Meanwhile the green water flow, another important part of water resources for the healthy development of rivers and basins, is seldom discussed. In arid and semi-arid regions, the analysis of spatiotemporal distribution of blue and green water resources under human activities and climate variability is critical for water resources planning and management, and for harmonizing agricultural water use and eco-environmental water requirements. The Weihe River is the largest tributary of the Yellow River in China and an important water source for the Central Shaanxi Plain, which acts as the main driving force in the western economic development of China. However, this region also suffers great resource shortages. Ensuring sufficient freshwater resources supply is one of the most essential prerequisites for economic development and environmental protection in the Wei River Basin. Using the Soil and Water Assessment Tool (SWAT) model, this study investigated the spatiotemporal variations of blue and green water resources under different human activities (land use/cover change and irrigation) and climate variability scenarios during the 1980s-2000s for the Weihe River Basin. The results showed that: 1) Under the impact of land use/cover change, irrigation and climate variation, the blue water flow, green water flow and green water storage decreased by 23.56 mm/a, 39.41 mm/a and 17.98 mm/a, respectively, during 1980-2009. Blue water flow and green water storage presented an increasing trend in the north of study area, and the green water flow showed a decreasing trend in the upstream regions. 2) Attribution analysis showed that climate variability accounted for a decrease of 13.17 mm/a, 44.99 mm/a and 22.79 mm /a in blue water flow, green water flow, and green water storage, respectively. The blue water flow increased in the north of the Weihe River Basin, but decreased in the south of the Weihe River Basin. The green water flow decreased in the whole basin. Land use/cover change accounted for a decrease of 0.42 mm/a and 0.37 mm/a respectively in blue water and green water flow, but an increase of 0.79 mm/a in green water storage. In addition, irrigation accounted for a decrease of 9.97 mm/a in blue water flow and an increase of 5.95 mm/a and 4.02 mm/a in green water flow and green water storage, respectively. 3) Green water coefficient showed an increased trend in the southeast, but a deceased trend in the Jinghe River Basin due to the climate variability. Land use/land cover change drived the green water coefficient increased in some sub-basins of southwest. It should also be noted that the green water coefficient significantly increased in Central Shaanxi Plain when considered the irrigation factor.