The impact of stored water on estimates of transpiration from scaled sap flux measurements was assessed in mature Pinus taeda (L.) at the Duke Free-Air CO(2) Enrichment (FACE) site. We used a simple hydraulic model with measurements of sap flux (J) at breast height and the base of the live crown for 26 trees over 6 months to examine the effects of elevated CO(2) (eCO(2)) and fertilization (N(F)) treatments, as well as temporal variation in soil moisture (M(()(t)())), on estimates of the hydraulic time constant (κ). At low M(()(t)()), there was little (<12%) difference in κ of different treatments. At high M(()(t)()), differences were much greater, with κ reductions of 27, 52 and 34% in eCO(2), N(F) and eCO(2) × N(F) respective to the control. Incorporating κ with these effects into the analysis of a larger data set of previous J measurements at this site (1998-2008) improved agreement between modeled and measured values in 92% of cases. However, a simplified calibration of κ that neglected treatment and soil moisture effects performed more dependably, improving agreement in 98% of cases. Incorporating κ had the effect of increasing estimates of reference stomatal conductance at 1 kPa vapor pressure deficit (VPD) and saturating photosynthetic active radiation (PAR) an average of 12-14%, while increasing estimated sensitivities to VPD and PAR. A computationally efficient hydraulic model, such as the one presented here, incorporated into a hierarchical model of stomatal conductance presents a novel approach to including hydraulic time constants in estimates of stomatal responses from long-term sap flux data sets.