Knowledge of water absorbed by caliche nodules is important for accurate soil water estimation. Simulated soil column experiments are used to investigate the effects of caliche nodules on soil profile water distribution and soil water estimation under given water supply conditions. The results indicate that for the treatments with five caliche nodules contents (CNC = 0, 10, 20, 30, and 40%), except for the top 0–0.1 m soil layer, the soil water content (SWC) of other layers is significantly different between the treatments (P < 0.05). The SWC is positively correlated to CNC. There are significant differences (P < 0.05) in caliche nodule water content (CWC) in the top three soil layers for all treatments. For soils with less than 10% caliche nodules, the soil water storage (SWS) in deeper soil layer (0.3–0.4 m) is significantly higher than that in surface soil layers (P < 0.05). Caliche nodule water storage (CWS) and available caliche nodule water storage (ACWS) both increase with increasing CNC. Water storage in the caliche nodules increases with the increase in CNC. There are significant differences in ACWS among soil layers in all soils (P < 0.05). The total ACWS significantly increases with the increase in CNC (P < 0.01). If water is absorbed by caliche nodules, then the total water storage of soils with CNCs of 10, 20, 30, and 40% would be underestimated by 3, 8, 10, and 17%, respectively. This study contributes to accurate soil water estimation in soils with caliche nodules and provide a scientific basis for rational utilization of soil and water resources.