An empirical model was used to predict the runoff of Shule river from 2011to 2050 based on climate model products with three emissions scenarios (A1B, A2 and B1). The coupled surface water and groundwater model were used to simulate and analyze the impacts of climate change and human activities on water resources allocation, groundwater system and ecological environments based on the predicted runoff. The following conclusions were drawn. For the three emissions scenarios in the future, temperature will dramatically increase, precipitation will decrease firstly and then increase, and runoff will decrease firstly and then increase compared with the value in 2000s decade, among which, A1B shows the biggest increase and B1 shows the smallest increase. Water supply quantity and structure in the future will be almost the same with those of 2010. Under control of human activities, canal infiltration, field return flow, and groundwater pumping show little differences among the three scenarios. Variation of river infiltration, groundwater evaporation, spring outflow will be consistent with that of runoff. Groundwater storage will decrease first then increase compared with 2010 level. By 2050, groundwater storage will increase for A1B and A2, but will decrease for B1. The area suited for natural plant growth will decrease for all the three scenarios. Vegetation degradation will be mainly concentrated in the southeast part of the plain.