The experiment was conducted in a completely randomized design in three water conditions at greenhouse with treatments as: control, water stress (water deficiency) and flooding (with a blade of water about 5 cm above the ground), and 15 repetitions. The analysis of variance was done and the 5% level of significance of the Tukey's test accomplished to assess the biochemical and physiological parameters of Hymenaea courbaril L. The variables were: water potential, nitrate reductase activity, concentration of nitrate, ammonium free, proline, glycine betaine, free protein, free amino acids, glutamine synthetase activity, alcohol dehydrogenase activity and lactate dehydrogenase and contents of chlorophyll a, b, and total carotene. There was a reduction of the enzyme reductase activity of nitrate and glutamine synthetase due to the water deficit and flooding. Moreover, the lack of water in leaf tissue caused an increase in proline, glycine betaine and free amino acids, trying to promote osmotic adjustment. An increase of variation and reduced ammonium, protein, chlorophyll a, b, and carotenoid was also observed. These substances were significantly reduced by the lack of water and also excess water. Thus, the water deficit and flooding promoted a drastic change in behavior and physiological biochemistry of Jatoba plants. The results of this study show that the flooding and water deficiency for 30 days are sufficient to promote changes in biochemical behavior in the Jatobá plants. Thus, these results indicate that the Hymenaea courbaril L. plants are less susceptible to flooding than to the water deficiency.