Water resources allocation decision-making in an arid region should consider the interaction of the economy, the environment, society, resources and other factors. In this paper, an index system for the comprehensive evaluation of water resources allocation in arid areas is established in response to the shortage of water resources, over-utilization of groundwater, and an unreasonable structure of agricultural water demand in the arid region of northwest China. It has been formulated based on current river basin water resources allocation practices and consideration of the fairness, efficiency and resource utilization rationality of water resources allocation. The projection tracking dynamic clustering approach was applied to analyze alternative water resource allocation schemes in the Kiz River Basin. It is concluded that the evaluation results demonstrate the following: (1) The PPDC model takes the actual measured value of the index as the basis for comprehensive evaluation, and it avoids the bias caused by the subjective formulation of weights. An optimal allocation scheme that has higher annual comprehensive benefits can better serve regional water resources management. (2) A projection pursuit dynamic cluster approach can deliver results which are more objective and reliable than existing evaluation approaches for water resources allocation. (3) Grey correlation analysis and projection tracking dynamic clustering are basically consistent with the evaluation results for water resources allocation in the Kiz River Basin. This suggests that the projection pursuit dynamic cluster is suitable for the evaluation of water resources allocation schemes.