Soil moisture is a consideration for soil conservation, agricultural production and climate modelling. This article presents a simple method for estimating soil moisture storage under water stress and storage depletion conditions. The method is driven by the common agro-hydrologic variables of precipitation (PPT), irrigation (IRR) and evapotranspiration (ET). The proposed method is successfully tested for the 152 000 km2 floodplain region of Hai River Basin using 48 consecutive months (2003–2006) of data. Soil moisture data from global land data assimilation system/Noah land surface model are validated with ground-truth data from 102 soil moisture monitoring sites. The validated soil moisture is used in combination with in situ groundwater data to quantify total water storage change (TWSC) in the region. The estimated storage change is in turn compared with gravity recovery and climate experiment-derived TWSC for the study area. The soil moisture and TWSC terms show favourable agreements, with discrepancies of < 10% on the average. While there is no consistent seasonal trend in soil moisture, TWSC shows a strong seasonality. It is low in spring and high in summer. This trend corresponds with the IRR–PPT season in the study area. Change in groundwater and total water storage indicates storage depletion in the basin. Storage depletion in the region is driven mainly by groundwater IRR and ET loss. Despite the low PPT and high ET, there is narrowing seasonal trend in soil moisture. This is achieved at the expense of groundwater storage. IRR pumping has induced extensive groundwater depletion in the basin. It is therefore vital to develop cultivation strategies that aim at limiting IRR pumping and ET loss. Water management practices that not only reduce waste but also ensure high productivity and ecological sustainability could also mitigate storage depletion in the region. These measures could reduce further not only the seasonal trend in soil moisture but also that in groundwater storage. Copyright © 2011 John Wiley & Sons, Ltd.