Glacial changes have great effects on regional water security because they are an important component of glacierized basin runoff. However, these impacts have not yet been integrated and evaluated in the arid/semiarid inland river basins of western China. Based on the degree-day glacier model, glacier changes and their hydrologic effects were studied in 12 subbasins in the Shiyang River basin (SYRB), Heihe River basin (HHRB) and Shule River basin (SLRB). The results showed that the glacier area of each subbasin decreased by 16.7–61.7% from 1965 to 2020. By the end of this century, the glacier areas in the three basins will be reduced by 64.4%, 72.0% and 83.4% under the three climate scenarios, and subbasin glaciers will disappear completely after the 2070s even under RCP2.6. Glacial runoff in all subbasins showed a decreasing–increasing–decreasing trend, with peak runoff experienced in 11 subbasins during 1965~2020. The contribution of glacial meltwater to total runoff in the basin ranged from 1.3% to 46.8% in the past, and it will decrease in the future due to increasing precipitation and decreasing glacial meltwater. However, the scale differences in glacier runoff are significant when aggregated over the region/basin/subbasin. This suggests that the results of large-scale generalization may be misleading for subbasin glacier water resource evaluations. Therefore, the hydrological effects of glaciers should be studied more in subbasins to provide an accurate reference for practical water resource management. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.