Seasonal variation of above ground and belowground biomass of Spartina maritima and Halimione portulacoides, decomposition rates of belowground detritus in litterbags, and carbon partitioning in plant components and sediments were determined in two Tagus estuary marshes with different environmental conditions. Total biomass was higher in the saltier marsh from 7,190 to 6,593 g m−2dw and belowground component contributed to more than 90%. Litterbag experiment showed that 30 to 50% of carbon is decomposed within a month (decomposition rate from 0.024 to 0.060 d−1). Slower decomposition in subsequent periods agrees with accumulation of carbon concentration in sediment. Atmospheric carbon annually transferred to the plant belowground biomass is stored more efficiently in sediments of Corroios than Pancas.