Physiological information about native species, make it possible to know their potential for use in programs to recovery degraded areas. Nowadays climate changes are severe and factors as water and light are involved with plant development and growth. We hypothesized that shading may contribute to adjusting the characteristics of photosynthetic metabolism of Campomanesia xanthocarpa seedlings under flooding. Thus, this work aimed to evaluate the flooding times and shading levels for gas exchanges and the maximal photochemical efficiency of PSII (Fv/Fm) in C. xanthocarpa seedlings. Seedlings were grown under two water regimes (control and flooding), three levels of shading (0, 30, and 70%) and 4 evaluation periods (0, 15, 30, and 45 days). We verified damages to the photosynthetic apparatus and reductions in the efficiency of the photochemical process under flooding and at a high level of shading (70%) in a short period (15 days). However, seedlings showed favourable responses to the adjustment over the 45 days of exposure to those conditions. According to the multivariate analysis, it was possible to identify the relation between photosynthetic rate and stomatal conductance as the main factor of metabolic adjustments in the tolerance of C. xanthocarpa to flooding and high shading intensity. C. xanthocarpa was more sensitive to short periods of flooding conditions and full sun and high level of shading (70%), however, it presented better adjustment responses to flooding periods when associated with 30% shade.