Spatiotemporal variability in soil water storage (SWS) is controlled by different factors operating at various intensities and scales. The traditional Pearson’s correlation analysis can be used to identify the linear correlations at the measurement scale only. In this study, wavelet coherency analysis was used to investigate scale-specific relationships between SWS and selected controlling factors. SWS of 135 sampling locations were calculated along a 1,340-m long sampling transect established in a typical catchment on the Loess Plateau, China. The selected controlling factors were soil saturated hydraulic conductivity (Ks); clay, silt, sand, and soil organic carbon (SOC) contents; elevation; and aboveground biomass (AGB). The spatial pattern of SWS measured in growing and nongrowing seasons and at different soil depths was similar. At all the sampling points, except for some locations in the depression area, SWS in the growing season was relatively greater than that in the nongrowing season. The influence of factors on SWS varied with scale, with soil Ks, clay and sand contents significantly correlated with SWS at large scales. Season and soil depth had no significant effect on scale-specific relationships between SWS and the controlling factors. The wavelet coherency analysis identified the type of correlation at different scales and locations. The outcomes of this study offer meaningful insights into the hydrological processes that can be observed in the Loess Plateau region and could have significant implications for future hydrological systems and water resources management.