Water storage in the unsaturated zone is a major determinant of the hydrological behaviour of the soil, but methods to quantify soil water storage are limited. The objective of this study is to assess the applicability of clay soil surface elevation change measurements to estimate soil water storage changes. We measured moisture contents in soil aggregates by EC-5 sensors, and in volumes comprising multiple aggregates and intra-aggregates spaces by CS616 sensors. In a prolonged drying period, aggregate-scale storage change measurements revealed normal shrinkage for layers = 30 cm depth, indicating volume loss equalled water loss. Shrinkage in a soil volume including multiple aggregates and voids was slightly less than normal, due to soil moisture variations in the profile and delayed drying of deeper soil layers upon lowering of the groundwater level. This resulted in shrinkage curve slopes of 0.89, 0.90 and 0.79 for the layers 0–60, 0–100 and 0–150 cm. Under a dynamic drying and wetting regime, shrinkage curve slopes ranged from 0.29 to 0.69 (EC-5) and 0.27 to 0.51 (CS616). Alternation of shrinkage and incomplete swelling resulted in an underestimation of volume change relatively to water storage change, due to hysteresis between swelling and shrinkage. Since the slope of the shrinkage relation depends on the drying regime, measurement scale and combined effect of different soil layers, shrinkage curves from laboratory tests on clay aggregates require suitable modifications for application to soil profiles. Then, the linear portion of the curve can help soil water storage estimation from soil surface elevation changes. These elevation changes might be measurable over larger extents by remote sensing.