The below ground biomass of salt marsh species accounts for more than half of the total plant biomass in salt marsh systems, yet no biomass data exist for salt marsh species in South Africa. The aims of the current study were to compare the biomass allocation of Salicornia tegetaria in six estuaries and relate findings to their environmental conditions. The current study measured the physico-chemical variables of the sediment (moisture content, organic matter content, electrical conductivity, pH) and pore water (temperature, salinity, pH, depth) at Olifants, Berg, Langebaan, Heuningnes, Nahoon and Kwelerha estuaries. Above and below ground biomass and stem height measurements were also collected. The below ground biomass (1.51 ± 0.24 kg m−2) and root/shoot ratio (1.36 ± 0.17) was the lowest at Heuningnes Estuary with no significant difference at the remaining estuaries, suggesting that factors, such as geomorphology and sedimentological processes, could have a stronger effect on the biomass allocation in this species. Important drivers of biomass allocation were sediment pH, redox potential and pore water depth. The current study provides baseline information for S. tegetaria, an endemic salt marsh species, for which there is a paucity of data. This species plays a major role in the ecology of the lower intertidal zone, which will be vulnerable to sea-level rise.