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Cerrado, constituting native Brazilian vegetation in the tropical and subtropical grasslands, savannas, and shrublands biome, has been extensively replaced by crop and pastureland, resulting in reduced water recycling to the atmosphere via evapotranspiration (ET). Re-introducing trees via integrated land-use systems potentially restores soil health and water-related processes; however, field data are scarce. During two years, we monitored soil moisture dynamics of natural Cerrado (CER), continuous pasture (COP), integrated crop-livestock (ICL), and integrated crop-livestock-forestry (ICLF) systems across 100 cm soil depth. Across years, mean soil moisture was highest for ICL, followed by COP and lowest in systems with trees (ICLF and CER). However, seasonal and spatial analyses revealed pronounced differences between soil layers and systems. COP and ICL mainly lost water from upper soil layers, whereas in ICLF, the strongest water depletion was observed at 40–100 cm depth, almost reaching a permanent wilting point during the dry season. CER was driest in the upper 40 cm, but water storage was highest below 60 cm depth. Our results suggest that compared to conventional land-use practices, integrated systems, including trees, increase water recycling to the atmosphere via ET and potentially compensate for the loss of key ecological functions of degraded or replaced Cerrado.