We have investigated the composition of the mobile natural organic matter (NOM) present in Callovo-Oxfodian pore water using electrospray ionization mass spectrometry (ESI-MS), atmospheric pressure chemical ionization mass spectrometry (APCI-MS) and emission-excitation matrix (EEM) spectroscopy. The generation of knowledge of the composition, structure and size of mobile NOM is necessary if one wants to understand the interactions of these compounds with heavy metals/radionuclides, in the context of environmental studies, and particularly how the mobility of these trace elements is affected by mobile NOM. The proposed methodology is very sensitive in unambiguously identifying the in situ composition of dissolved NOM in water even at very low NOM concentration, due to innovative non-disturbing water sampling and ionization (ESI/APCI-MS) techniques. It was possible to analyze a quite exhaustive inventory of the small organic compounds of clay pore water without proceeding to any chemical treatment at naturally occurring concentration levels. The structural features observed were mainly acidic compounds and fatty acids as well as aldehydes and amino acids.