Measurements of stomatal conductance and transpiration can provide information on plant carbon gain and water loss, which can easily be used to estimate a plant's ability to tolerate flooding. In this study, flooding-sensitive Sorghum halepense and flooding-tolerant Phragmites australis were flooded to 8 cm depth or kept dry for 7 days. Transpiration, stomatal conductance, boundary layer conductance, and vapor conductance were measured for each. In S. halepense, transpiration was significantly higher in dry treatments compared to flooded treatments. However, in P. australis transpiration was significantly higher in flooded treatments compared to dry treatments. Boundary layer conductances were not different between species or treatments. Phragmites australis had increased stomatal conductance when flooded, which indicates a high physiological tolerance to waterlogged soils. By contrast, stomatal conductance in S. halepense was decreased under flooding, indicating a greater sensitivity to flooding. Based on these differences between P. australis and S. halepense, leaf-level stomatal conductance appears to serve as a quick indication of flooding tolerance in plants.