Deep seawater (DSW), defined as seawater deeper than 200 m, has notable applications in various fields such as energy, agriculture, food, cosmetics, and public health. Several studies have attributed its utility to mineral effects; however, its organic compounds have rarely been investigated. To support mechanistic evidence related to DSW, a sensitive analytical method was developed for the individual analysis of d- and l-amino acids (AAs) using enantiochemical tagging-liquid chromatography-tandem mass spectrometry. A novel reagent, 2,4-dichloro-6-methoxy-1,3,5-triazine-d-leucine, was developed to enable high-speed analysis of individual dl-AAs, allowing quantification of 19 proteogenic and 2 nonproteogenic dl-AAs within 17 min. Furthermore, this reagent facilitated rapid tagging of target AAs within 10 min of reaction. A limit of detection of 10-100 pmol/L (in vial) was achieved, which was sufficient to characterize the dl-AA profiles in DSW. Three batches of DSW from Toyama Bay were quantitatively analyzed using the spiking standard method, revealing dl-AA concentrations of 10-100 nmol/L. Notably, d-leucine, d-valine, d-alanine, d-serine, d-threonine, and d-glutamic acid were detected at higher concentrations than other d-AAs. A lifespan assay using the Caenorhabditis elegans model demonstrated that DSW exhibited a clear proliferative effect, similar to the positive control. Moreover, dl-AA analysis revealed a reduction in d-aspartic acid, an established aging marker, in the proliferated groups.