<p>Prolonged drought stress at mild/moderate intensities is assumed to be a realistic situation that natural tree populations will face in the future warming climate. Here we performed a six-week experiment during which water supplies were controlled by applying a repeated cycle of intermittent watering to the current-year seedlings of <i>Fagus crenata</i> originating from two snowy regions in Japan, in order to examine the effects of moderate, prolonged, but gradual, soil drought stress on them as well as to determine any site-common and/or -specific patterns. Compared to the well-watered seedlings, there were no or limited changes in stomatal conductance, leaf water content, root-to-shoot ratio, and concentrations of total soluble sugar and free-proline in leaves of the seedlings that received intermittent watering over the three census dates. In contrast, the seedlings from both sites that received intermittent watering exhibited significant increases in the concentration of malondialdehyde in leaves on every census date, compared to well-watered seedlings. There were very few notable between-site differences in any of the phenotypic traits mentioned above. Due to the moderate intensity of drought stress combined with unexpectedly high vapor pressure deficit and low light intensity in the greenhouse, we detected neither drought stress-driven stomatal closure nor cellular osmotic balancing; however, reactive oxygen species may have been produced in leaves of the seedlings. These findings imply that the concentration of malondialdehyde is a promising candidate biochemical marker for detecting early signs of adverse effects on <i>F. crenata</i> seedlings under soil drought conditions in the future warming climate.</p>