ABSTRACT Soil water saturation requires different adaptative strategies by tree species that live under such conditions. We aimed to study the responses that ensure flooding tolerance by tree species and so provide support for recovery projects with degraded areas subject to flooding. We evaluated the ecophysiology of Cedrela fissilis under different water saturations, including anatomical traits, gas exchange parameters, antioxidant system analysis and growth. We subjected 100 day-old plants to three treatments: Control (FC) where the substrate was kept at field capacity; Flooded Roots (FR), where the substrate remained submerged but with no surface layer of water, and Flooded Stem (FS), with a water layer accumulation of around 3.0 cm over the substrate, flooding part of the stems. The plants were kept under such conditions for 90 days. Plants survived in all treatments due to a marked development of cortical intercellular spaces in flooded plants. However, photosynthesis and other gaseous exchange were limited under FR and FS treatments. In addition, the periderm thickness was reduce by flooding and there was an accumulation of starch grains in the parenchyma cells of the xylem, cortex and pith of the stem. There was also a significant lipid peroxidation on the leaves under FR and FS treatments. The superoxide dismutase activity was decreased, but the activities of the ascorbate perioxidases and catalase in the leaves were increased. We concluded that young Cedrela fissilis plants partially tolerate flooding since they developed ecophysiological changes in order to survive in this condition. Consequently, this species is a good candidate for the reforestation projects in environments where intermittent flooding occurs, such as riverside and riparian forests.