We used electrical impedance spectroscopy (EIS) to measure leaves and stems of white birch (Betula platyphylla) under different periods of simulated flooding stress and determined the water content and membrane permeability of leaves and stems. The correlation between water content and membrane permeability with parameters of the EIS in leaves and stems was analyzed. Using linear and non-linear regression with some data, we built models of water content of leaves and stems under flooding stress. The waterlogging tolerance time of white birch was assessed by EIS and electrolyte leakage methods. The water content of leaves and stems increased with increasing duration of flooding stress. In leaves, the reactance value in the EIS top arc decreased under flooding stress, and in stems, the reactance value in the EIS top arc increased first, then decreased. Under flooding stress, the water content and membrane permeability were correlated with some parameters of the EIS in leaves and stems. The specific high-frequency resistance parameter (r) of EIS best estimated the water content of leaves and stems. The prediction accuracy of the models was 84.30% and 94.34% for leaves and stems, respectively. Therefore, EIS data can be used to assess the water content in leaves and stems of birch under flooding stress, and the models established in this paper have good reliability and applicability for water content estimation. In addition, white birch could tolerate at least 30 days of flooding. EIS technology might be used to monitor the physiological status and growth trend of trees under adverse conditions.