Maintaining the water balance of soil-vegetation systems is necessary for the ecological restoration of desertified regions. However, the major processes controlling water balance after revegetation remains unclear. To quantify the water balance after revegetation of moving sand dunes, we performed an 18-year-long large-weighting lysimeter monitoring study in the Tengger Desert, northern China. We measured daily precipitation, evapotranspiration (ET), and drainage loss (DL) on an area revegetated with either Artemisia ordosica or Caragana korshinskii, two shrubs with different crown size and rooting depth, and with bare soil. Our results showed that the annual precipitation of 186 mm was partitioned to 64% evaporation and 23% DL on the bare soil control. However, the water balance changed after revegetation, with the vast majority of precipitation ending up as ET (93% in A. ordosica and 98% in C. korshinskii). The relationships of ET and DL with precipitation showed a quasi-steady state at annual scales, a varying state at seasonal scales, and a pulsed state at daily scales. We also observed spatiotemporal niche partitioning between the two shrubs, where differences in water use promoted their coexistence in the revegetated desert areas. Our study suggests that the density and area of revegetation should be controlled within a certain range in accordance with the underlying soil-vegetation water balance in desert regions. Otherwise, sand-binding revegetation would be degraded and the ecological benefits of dune fixation would be lost.