Hydrogen isotope ratios (2H/1H or δ2H) of plant leaf waxes typically covary with those of precipitation, and are therefore used as a proxy for past hydrologic variability. Mangroves present an important exception to this relationship, as salinity can strongly influence 2H fractionation in leaf lipids. To better understand and calibrate this effect, δ2H values of taraxerol and n-alkanes were measured in the leaves of Rhizophora spp. (red mangroves) from three estuaries and four brackish lakes on the Micronesian islands of Pohnpei and Palau, and compared to the δ2H and δ18O values of leaf water, xylem water and surface water. Net 2H discrimination between surface water and taraxerol increased by 0.9±0.2‰ per part per thousand (ppt−1) over a salinity range of 1–34ppt. Xylem water was always depleted in 2H relative to surface water, and the magnitude of this depletion increased with salinity, which is most likely due to a combination of greater 2H discrimination by roots during water uptake and opportunistic use of freshwater. Changes in the 2H content of xylem water can account for up to 43% of the change in net taraxerol fractionation with salinity. Leaf water isotopes were minimally enriched relative to xylem water and there was not significant variability in leaf water enrichment with salinity, which is consistent with a Péclet-modified Craig–Gordon model of leaf water enrichment. As leaf water enrichment is therefore unlikely to be responsible for increased 2H/1H fractionation in mangrove leaf lipids at elevated salinities, the majority of this signal is most likely explained either by changes in biosynthetic fractionation in response to salt stress or by salinity influenced changes in the timing of water uptake and lipid synthesis.