The euhalophyte species Salicornia europaea is cultivated for oilseed and as a fodder crop in various parts of the world. In saline coastal environments it possesses great potential for the subsistence of the most disadvantaged farmers. We investigated the effect of salinity levels in irrigation water on the germination capacity, shoot biomass and seed productivity as well as diverse quality traits (nitrogen content in shoots and seeds and fatty acids, in seeds) and physiological traits (stable carbon and nitrogen isotopes and ion content) of two accessions collected in the United Arab Emirates (UAE). The three salinity levels tested were irrigation with fresh water, brackish water and sea water. In addition, a hypersaline condition was also tested for germination. The best germination rates were achieved with seeds exposed to fresh and brackish water, while imbibition with sea water decreased germination by half and hypersaline water inhibited it almost totally. However, the best irrigation regime in terms of biomass and seed yield involved brackish water. Moreover, rising salinity in the irrigation increased the stable isotope composition of carbon (δ13C) and nitrogen (δ15N), together with the Na+ and K+ of shoots and seeds, and the lipid levels of seeds, while the total nitrogen content and the profile of major fatty acids of seeds did not change. Differences between the two ecotypes existed for growth and seed yield with the best ecotype exhibiting lower δ13C and higher K+ in both shoots and seeds, lower Na+ and higher 15N in shoots, and lower N in seeds, together with differences in major fatty acids. Physiological mechanisms behind the response to irrigation salinity and the ecotypic differences are discussed in terms of photosynthetic carbon and nitrogen metabolism.