Water scarcity, intensified by climate change, limits the growth and survival of threatened tree species, such as Paubrasilia echinata (Lam.) Gagnon, H.C.Lima & G.P.Lewis. This study analyzed the effects of water availability in the soil on the morphophysiology and enzymatic activity of P. echinata seedlings under different irrigation intervals. The experiment consisted of five treatments (irrigation intervals: 0, 3, 6, 9, and 12 days) distributed in four randomized blocks, totaling 20 plots of five plants each. Variables analyzed included stem diameter, number of leaves and leaflets, leaf area, shoot and root length, root volume, dry matter mass, Dickson quality index, relative water content, leaf indices of chlorophyll, peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase. Water deficit reduced root dry matter mass by up to 27.78% and chlorophyll b by up to 29.56%, and increased peroxidase by up to 244.44%. Principal component analysis revealed correlated changes among biomass, chlorophyll, and Dickson index, with root volume and enzymatic activities varying oppositely, indicating an integrated regulatory response. P. echinata exhibits phenotypic plasticity under water deficit, reflected in stem diameter, root volume, leaf area, physiological traits, and enzymatic regulation, tolerating an irrigation interval of 12 days. P. echinata has establishment potential in areas subjected to water deficit.