The summertime flowers of the ever-flowering Meiwa kumquat (Fortunella crassifolia Swingle) are the most useful for fruit production in Japan; however, summertime flowers bloom in three or four successive waves at approximately 10 day intervals, resulting in fruit of different maturity occurring on the same tree. Soil water deficit (SWD) treatment has been shown to reduce the flowering frequency and improve harvest efficiency; therefore, in this study, the effects of SWD treatment on the accumulation of soluble sugars in each tree organ above-ground were examined and it was discussed how SWD affects the whole-tree water relations and sugar accumulation by osmoregulation. The number of first-flush summertime flowers was higher in SWD-treated trees than non-treated control (CONT) trees (177.0 and 58.0 flowers, respectively), whereas the second- and third-flush flowers were only observed in CONT trees. The soluble sugar content was higher in SWD treated trees than CONT trees for all organs and tended to be higher in current-year organs than previous-year organs; however, when the sugar content of the current-year spring stems exceeded approximately 100 mg g−1 dry weight, the current-year leaf water potential decreased sharply and the rate of increase in the number of first-flush flowers also tended to decrease. SWD treatment significantly increased the total sugar content of the xylem tissue of the scaffold branches to three times the value in CONT trees (p = 0.001); however, the increase was observed even in sucrose, a disaccharide, similar to that in monosaccharides such as glucose and fructose. These results suggest that the increased sugar levels in the xylem tissue resulted from not only osmoregulation but also other factors as well; therefore, these sugars may affect whole-tree water relations as well as the development of flower buds.