The concentrated deep seawater has been discharged abundantly in the processes manufacturing many kinds of goods from the deep seawater. In this study, a suitable application of the concentrated deep seawater for the high quality tomato production was examined. Tomato plants (Lycopersicon esculentum Mill.) were grown in the NFT system and the hydroponic pots, where the concentrated deep seawater was applied for the short-term salt stress treatment for only two weeks at the stage of rapid fruit growth. Physiological effects of the application of the concentrated deep seawater were analyzed with special reference to osmoregulation in the phloem transport, antioxidant system, amino acid metabolism and fruit quality. From these physiological analyses, it was verified that the short-term application of the concentrated deep seawater at the stage of rapid fruit growth can induce the osmoregulation in the phloem transport and the antioxidant system, which can produce high quality tomatoes enriched in sugar, minerals, functional amino acids and good flavour without occurrence of extremely small-sized fruits and blossom-end rot.