The influence of different concentrations (10-2000μM) of heavy metals (Cu, Mn, Ni, Zn) was analysed in Atriplex halimus and Salicornia ramosissima germination pattern and seedling size. They are two halophyte species that grow in the Estuary of Huelva (Southwest Iberian Peninsula, Spain), one of the most heavy metal-polluted environments in the world. All of the metals tested affected the final germination percentage in A. halimus and only Ni reduced germination in S. ramosissima. The germination rate was unaffected in both species. The study of seedling development shows that S. ramosissima, an intertidal annual species, has a higher tolerance of metals than A. halimus, a bush that inhabits the upper part of the marshes. Taking into account the metal concentrations in the estuary and the effects of these on the seedling development of the species analysed, we conclude that metals might limit plant colonisation in some parts of the marshes.