In this paper, multiple data sources (including weather, soil, land use, and digital elevation data) from 1980 to 2012 were applied to drive the SWAT model. The hydrological process was modeled at the county scale, and the spatio-temporal changes in water resources were analyzed with the model outputs in the arid northwestern county of Linze county. The results showed that annual mean evaporation, infiltration, lateral recharge, underground recharge, water yield, available surface water, and yield coefficient were 130.53 m, 49.78 mm, 68.95 mm, 48.00 mm, 53.47 mm, (13.17 ±0.60)×10⁸ m³, and 0.16 during 1980-2012, whereas the average annual ecological consumption of water was (3.56 ±0.12)×10¹¹ m³ and presented an increasing trend. Further analysis indicated that the lateral recharge and underground recharge were the controlling factors of water yield, whose contributions were 43% and 57%, respectively. Moreover, the results showed that hydrological processes were driven mainly by the scheme of "water diversion in Heihe River", and all of abrupts for hydrological elements occurred from 2000 to 2005. Spatially, actual evaporation, underground recharge, and yield coefficient across Linze county was higher in the south than in the north. Further analysis indicated that lateral recharge and underground recharge were the factors controlling the water yield, whose contributions were 43% and 57% respectively. Available surface water in the Linze during 1980-2012 was controlled by upstream inflow, which contributed up to 83%. In addition, our study found there was evaporation paradox during 2007-2012, which is attributed to the continual increase in actual evapotranspiration.