In desert basins where phreatophyte species are common, the contribution of groundwater evapotranspiration (ETg) and vadose zone ET (ETsoil) to total ET remains an important uncertainty. Here, ETg and ETsoil, and proportional contributions of each to total ET, were estimated for a phreatophyte (shrub)-dominated desert ecosystem in California, USA. ETg and ETsoil were estimated from a water balance approach using daily ET, daily precipitation and monthly vadose zone soil water storage (SWS) data collected across five sites and over 2 years. Precipitation was ~ 40% below average during the first year (2022) and ~ 110% above average during the second year (2023). Isotopic sampling of shrubs, soil and groundwater was also used to determine spatial and temporal changes in shrub water sources. We found that ETg/ET averaged 0.28 over the full 2-year period. On average, ETg/ET was higher in the dry year (0.36) than the wet year (0.22). Winter precipitation and summer rain events strongly influenced SWS and estimated ETg and ETsoil. Isotopic analysis indicated that shrubs used mostly vadose zone water (~ 50% to > 90%) when SWS was high or increasing, which were periods of peak shrub growth and high ET. Shrubs used mostly groundwater (40% to > 90%) when SWS was low or decreasing, which occurred during periods of limited growth and low ET. Our results highlight the importance of accounting for changes in SWS in estimates of ETg and ETsoil and demonstrate the influence of temporal changes in shrub water sources on vadose zone water and groundwater contributions to ET.