Changing climatic conditions and extensive human activities have influenced the global water cycle. In recent years, significant changes in climate and land use have degraded the watershed ecosystem of the Ebinur Lake Basin in Xinjiang, Northwest China. In this paper, variations of runoff, temperature, precipitation, reference evapotranspiration, lake area, socio-economic water usage, groundwater level and water quality in the Ebinur Lake Basin from 1961 to 2015 were systematically analyzed by the Mann-Kendall test methods (M-K) mutation test, the cumulative levelling method, the climate-sensitive method and land-use change index. In addition, we evaluated the effects of human activities on land use change and water quality. The results reveal that there was a significant increase in temperature and precipitation from 1961 to 2015, despite a decrease in reference evapotranspiration. The Wenquan station was not significantly affected by human activities as it is situated at a higher altitude. Runoff at this station increased significantly with climate warming. In contrast, runoff at the Jinghe station was severely affected by numerous human activities. Runoff decreased without obvious fluctuations. The contributions of climate change to runoff variation at the Jinghe and Wenquan stations were 46.87% and 58.94%, respectively; and the contributions of human activities were 53.13% and 41.06%, respectively. Land-use patterns in the basin have changed significantly between 1990 and 2015: urban and rural constructed lands, saline-alkali land, bare land, cultivated land, and forest land have expanded, while areas under grassland, lake, ice/snow and river/channel have declined. Human activities have dramatically intensified land degradation and desertification. From 1961 to 2015, both the inflow into the Ebinur Lake and the area of the lake have declined year by year; groundwater levels have dropped significantly, and the water quality has deteriorated during the study period. In the oasis irrigation area below the runoff pass, human activities mainly influenced the utilization mode and quantity of water resources. Changes in the hydrology and quantity of water resources were driven primarily by the continuous expansion of cultivated land and oasis, as well as the growth of population and the construction of hydraulic engineering projects. After 2015, the effects of some ecological protection projects were observed. However, there was no obvious sign of ecological improvement in the basin, and some environmental problems continue to persist. On this basis, this study recommends that the expansion of oasis should be limited according to the carrying capacity of the local water bodies. Moreover, in order to ensure the ecological security of the basin, it is necessary to determine the optimal oasis area for sustainable development and improve the efficiency of water resources exploitation and utilization.