The extent to which both water source and atmospheric humidity affect δ2H values of terrestrial plant leaf waxes will affect the interpretations of δ2H variation of leaf waxes as a proxy for hydrological conditions. To elucidate the effects of these parameters, we conducted a long-term experiment in which we grew two tree species, Populus fremontii and Betula occidentalis, hydroponically under combinations of six isotopically distinct waters and two different atmospheric humidities. We observed that leaf n-alkane δ2H values of both species were linearly related to source water δ2H values, but with slope differences associated with differing humidities. When a modified version of the Craig–Gordon model incorporating plant factors was used to predict the δ2H values of leaf water, all modelled leaf water values fit the same linear relationship with n-alkane δ2H values. These observations suggested a relatively constant biosynthetic fractionation factor between leaf water and n-alkanes. However, our calculations indicated a small difference in the biosynthetic fractionation factor between the two species, consistent with small differences calculated for species in other studies. At present, it remains unclear if these apparent interspecies differences in biosynthetic fractionation reflect species-specific biochemistry or a common biosynthetic fractionation factor with insufficient model parameterization.