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Plant ecophysiological trade-offs between different strategies for tolerating stresses are widely theorized to shape forest functional diversity and vulnerability to climate change. However, trade-offs between hydraulic and stomatal regulation during natural droughts remain under-studied, especially in tropical forests. We investigated eleven mature forest canopy trees in central Amazonia during the strong 2015 El Niño. We found greater xylem embolism resistance (P50 = − 3.3 ± 0.8 MPa) and hydraulic safety margin (HSM = 2.12 ± 0.57 MPa) than previously observed in more precipitation-seasonal rainforests of eastern Amazonia and central America. We also discovered that taller trees exhibited lower embolism resistance and greater stomatal sensitivity, a height-structured trade-off between hydraulic resistance and active stomatal regulation. Such active regulation of tree water status, triggered by the onset of stem embolism, acted as a feedback to avoid further increases in embolism, and also explained declines in photosynthesis and transpiration. These results suggest that canopy trees exhibit a conservative hydraulic strategy to endure drought, with trade-offs between investment in xylem to reduce vulnerability to hydraulic failure, and active stomatal regulation to protect against low water potentials. These findings improve our understanding of strategies in tropical forest canopies and contribute to more accurate prediction of drought responses.