The objective of this study is to assess the applicability of clay soil elevation change measurements to estimate soil water storage changes, using a simplified approach. We measured moisture contents in aggregates by EC-5 sensors, and in multiple aggregate and inter-aggregate spaces (bulk soil) by CS616 sensors. In a long dry period, the assumption of constant isotropic shrinkage proved invalid and a soil moisture dependant geometry factor was applied. The relative overestimation made by assuming constant isotropic shrinkage in the linear (basic) shrinkage phase was 26.4% (17.5 mm) for the actively shrinking layer between 0 and 60 cm. Aggregate-scale water storage and volume change revealed a linear relation for layers = 30 cm depth. The range of basic shrinkage in the bulk soil was limited by delayed drying of deep soil layers, and maximum water loss in the structural shrinkage phase was 40% of total water loss in the 0–60 cm layer, and over 60% in deeper layers. In the dry period, fitted slopes of the ¿V–¿W relationship ranged from 0.41 to 0.56 (EC-5) and 0.42 to 0.55 (CS616). Under a dynamic drying and wetting regime, slopes ranged from 0.21 to 0.38 (EC-5) and 0.22 to 0.36 (CS616). Alternating shrinkage and incomplete swelling resulted in limited volume change relative to water storage change. The slope of the ¿V–¿W relationship depended on the drying regime, measurement scale and combined effect of different soil layers. Therefore, solely relying on surface level elevation changes to infer soil water storage changes will lead to large underestimations. Recent and future developments might provide a basis for application of shrinkage relations to field situations, but in situ observations will be required to do so.