Although water table depth is commonly regarded as the primary determinant of litter decomposition rate in tropical peatlands, this has rarely been tested experimentally. This study explored the influence of flooding on decomposition of litter from three dominant plant species in a neotropical peatland. The non-flooded treatment reduced the mass remaining after 14 months from 84 to 81 % for Raphia taedigera, 65 to 58 % for Campnosperma panamensis, and 69 to 58 % for Cyperus sp. The proportions of carbon, nitrogen and phosphorus in the labile, semi-labile and recalcitrant carbon pools, did not reliably predict differences among species in the mass loss rate of litter. Phosphorus was rapidly lost from litter, while carbon losses, including soluble carbon, were slower, but significant for all fractions. The non-flooded treatment substantially reduced the quantity of C remaining in the residue fraction of leaf litter after 12 weeks, with 31, 19 and 6 % less remaining in the non-flooded treatment for R. taedigera, C. panamensis and Cyperus sp. This suggests that lower water table depth on litter decay increase degradation of mainly aliphatic and aromatic carbon in the residual fraction. Thus, although lowering the water table increased decomposition, the chemical composition of litter clearly influences peat accumulation.