Depletion of water resources has threatened water security in the Beijing-Tianjin-Hebei urban agglomeration, China. However, the relative importance of precipitation and urbanization to water storage change has not been sufficiently studied. In this study, both terrestrial water storage (TWS) and groundwater storage (GWS) change in Jing-Jin-Ji from 1979 to the 2010s were investigated, based on the global land data assimilation system (GLDAS) and the EartH2Observe (E2O) outputs, and we used a night light index as an index of urbanization. The results showed that TWS anomaly varied in three stages: significant increase from 1981 to 1996, rapid decrease from 1996 to 2002 and increase from 2002 to the 2010s. Simultaneously, GWS has decreased with about 41.5 cm (500% of GWS in 1979). Both urbanization and precipitation change influenced urban water resource variability. Urbanization was a relatively important factor to the depletion of TWS (explains 83%) and GWS (explains 94%) since the 1980s and the precipitation deficit explains 72% and 64% of TWS and GWS variabilities. It indicates that urbanization coupled with precipitation deficit has been a more important factor that impacted depletion of both TWS and GWS than climate change only, in the Jing-Jin-Ji region. Moreover, we suggested that the cumulative effect should be considered when discussing the relationship between influence factors and water storage change.