DISEQUILIBRIA within the mixture of organic matter, mineral particles and seawater in near-surface sediments result in extensive reaction, often biologically mediated. Variations in interstitial water composition are very sensitive indicators of the chemical and biological reactions in this zone of transition and the interaction between the water column and the permanent deposit1,2. Although most studies have been confined to inorganic ions, the few measurements of pore water DOC in marine sediments3–6 show large gradients in dissolved organic matter concentration within sediments and across the sediment–water interface. We describe here our study of dissolved amino acids in interstitial waters, which were used to trace some of the biogeochemical processes affecting organic matter in marine sediments. We have analysed the dissolved free amino acids in 15 interstitial water samples from four cores obtained in Buzzards Bay, Massachusetts; the Gulf of Maine; and the North-west Atlantic continental rise. These pore waters have very high amino acid concentrations, of the order of 1 mg l−1. In addition, the distribution of individual amino acids differs substantially from that reported for seawater7,8, particularly in the large relative abundance of glutamic acid and β-aminoglutaric acid. β-aminoglutaric acid (HOOCCH2CH(NH2)CH2COOH) is an isomer of glutamic acid which, to our knowledge, has not been previously reported in the marine environment.