BTEX (benzene, toluene, ethylbenzene, and the different xylene isomers), known for carcinogenic and neurotoxic effects, are common environmental contaminants. The first step for the development of the bioremediation technologies is the detection of intense microbial degradation in contaminated waters in the quest for the most active bacterial strains. This requires the multispecies analysis for BTEX metabolites which are considered as markers of microbial degradation. A direct (50 µL injection) HPLC–electrospray MS/MS analytical method was developed for the simultaneous analysis of 11 BTEX metabolites (o-, m-, p-toluic, salicylic, benzoate, benzyl, and phenyl succinic acids, 2-(1-phenylethyl)-, 2-(2-methylbenzyl), and 2-(3-methylbenzyl)-, 2-(4-methyl benzyl)-succinic acids) in bacterial cultures and ground waters down to 0.1 ng/mL. The optimization of the chromatographic conditions allowed for the resolution of position isomers of toluic and methylbenzyl-succinic acids. The stability of the analytes during sample storage tested in different conditions showed the instability of some of them when stored at room temperature. The feasibility of the method was demonstrated by the detection of all the investigated metabolites in a water sample of a deep aquifer hosting natural gas storage. A model laboratory study emphasized the importance of 2-(2-methylbenzyl)-succinic acid as a marker of anaerobic microbial degradation.