Hydrogen isotope ratios (²H/¹H, δ²H) of leaf waxes covary with those in precipitation and are therefore a useful paleohydrologic proxy. Mangroves are an exception to this relationship because their δ²H values are also influenced by salinity. The mechanisms underlying this response were investigated by measuring leaf lipid δ²H and leaf and xylem water δ²H and δ¹⁸O values from three mangrove species over 9.5 months in a subtropical Australian estuary. Net ²H/¹H fractionation between surface water and leaf lipids decreased by 0.5-1.0‰ ppt^-1 for n-alkanes and 0.4-0.8‰ ppt^-1 for isoprenoids. Xylem water was ²H depleted relative to surface water, reflecting ²H discrimination of 4-10‰ during water uptake at all salinities and opportunistic uptake of freshwater at high salinity. However, leaf water ²H enrichment relative to estuary water was insensitive to salinity and identical for all species. Therefore, variations in leaf and xylem water δ²H values cannot explain the salinity-dependent ²H depletion in leaf lipids, nor the 30‰ range in leaf lipid δ²H values among species. Biochemical changes in direct response to salt stress, such as increased compatible solute production or preferential use of stored carbohydrates, and/or the timing of lipid production and subsequent turnover rates, are more likely causes.