Hydrogen isotope ratios in lipids derived from mangroves have the potential to be used for paleohydrologic reconstructions and could serve as a much needed tool for establishing past climate variability in the tropics. We assessed the effect of salinity on the apparent fractionation factor, α_a, between mangrove derived n-alkanes and their source water for Avicennia marina (gray mangrove) specimens collected along a 28 PSU salinity gradient in the Brisbane River Estuary. Our results indicate that there is an inverse relationship between the apparent fractionation factor and salinity. This salinity effect is large enough to override variability in the isotopic composition of source water, which plays a dominant role in determining the hydrogen isotope ratio of leaf waxes in other vascular plants. We suggest that this relationship may be due to (i) increased discrimination against deuterium during water uptake at high salinity, (ii) increased production of compatible solutes from D enriched pyruvate at high salinity, resulting in more hydrogen from D depleted NADPH being incorporated in leaf waxes, and/or (iii) increased secretion of salty brine by leaves at high salinity, resulting in (iii.a) higher relative humidity at the leaf surface, and (iii.b) introducing the possibility that D depleted water of hydration is absorbed by the leaf. Our results indicate that hydrogen isotope ratios of mangrove lipid biomarkers can be developed as a paleosalinity indicator. They also imply that care must be taken when interpreting hydrogen isotopic variations in non-source specific higher plant lipids in sediments where both mangrove and non-mangrove plants contribute organic material.