For tropical tree species, wood density can vary greatly both within and between species depending on environmental conditions. In Amazonian seasonally flooded forests, yearly flood pulses influence tree growth and floodplain trees have developed specialised strategies to cope with prolonged submersion during flooding. We therefore hypothesised that seasonal floods significantly affect the capacity of trees to store carbon as woody biomass per unit volume and that forest hydrology would be an important factor in determining above-ground woody biomass and carbon stocks across the Amazon Basin. To test these hypotheses, we collected and analysed wood cores from 44 species occurring in both seasonally flooded (várzea) forests and adjacent unflooded (terra firme) forests along the Juruá River, western Brazilian Amazon. We used wood specific gravity (WSG) as a proxy of woody biomass and carbon. We compared WSG values within species, genera and families and found higher WSG in unflooded forest trees compared to their conspecifics in seasonally flooded várzea. Moreover, the effect of forest type on WSG was strongest at the family level and weakest at the species level. We further assessed the implications of WSG accuracy on above-ground woody tree biomass and found significant differences in AGWB as a function of WSG. Again, the differences became greater with lower taxonomic specificity, but also increased with lower site-specificity and greater tree dimensions. In conclusion, habitat specific WSG is important to quantify and map the spatial distribution of above-ground woody biomass and carbon in Amazonian forests.