Understanding the behavior of the groundwater body and its long term trends is essential for making any management decision in a given watershed. This paper made an estimation of the groundwater resources variation in the Zhangye Basin during 1985-2013 based on the long-term groundwater observation data and geostatistical method by partitions according to the different ways of irrigation. The results show that groundwater level and storage exhibit tremendous dissimilarity on temporal and spatial scale for the whole Zhangye Basin. The accumulative groundwater storage decreased by nearly 47.52 ×108 m3 , the annual average deficit reached 1.64 ×108 m3 , among which the accumulative groundwater level drawdown in the river/well water mixed irrigation district reached 5.72m, groundwater storage decreased by 37.48 ×108 m3 , accounting for about 78.87% of the total water loss of the Zhangye Basin. Accumulative groundwater level drawdown changed from high to low order in respective partitions: river water ﹥river and well water mixed ﹥ spring water ﹥ river and spring water mixed ≥ well water irrigation district, and the corresponding accumulative storage variation is: river and well water mixed ﹥river water﹥well water﹥river and spring water mixed﹥well water irrigation district. In the long-temporal scale, multi-year accumulative storage in these partitions is still in negative change, namely the groundwater resource is still in a rather severe deficit, which would make a great threat to the aquifer. This is the result from the joint action of climate change and human activities, and human activities such as water diversion policy, groundwater mining and water saving project have become greater and greater. This study may provide a scientific basis for water resources planning and scheduling and provide relatively reliable way of estimating large scale groundwater balance.