The seasonal flood pulse characteristic of Amazonian floodplains (várzeas) has direct effects on vegetation, influencing the physiological aspects of the species, such as stomatal conductance (gs). This study aimed to analyze the ecophysiological behavior regarding the stomatal conductance (gs) aspect of seven native plant species of Amazonian floodplain ecosystem in two distinct seasons (rainy and dry season) and in two topographic environments (high and low floodplain). The gs readings performed on healthy leaves with the aid of an AP4 Porometer at three different times throughout the day. The results showed high physiological plasticity in the studied species, where the process of water regulation by the leaf stomata exhibits a distinct behavior between the dry and rainy periods. It was more homogeneous during the dry period, where there was a reduction in gas rates. N. macrophylla was the most tolerant species to water deficit of the dry period and S. reticulata the most sensitive. The most tolerant species to flooding was C. tapia and the most sensitive G. brasiliensis. These results suggest different ecophysiological behaviors of native Amazonian floodplain species, suggesting different management practices in the face of local and global climate change.