Aquifer system and depth specific chemical patterns in fractured-rock groundwater from the Critical Zone revealed by untargeted LC-MS-based metabolomics

•Groundwater metabolomics reveals below ground biogeochemical processes.•Mass spectrometry identifies patterns of DOM fluxes and transformations in the aquifer.•Input of DOM by above-ground processes, transformation and transport can be distinguished.•Marker-free work allows identification of microbial contributions to DOM structure.•Land-use type, aquifer system, and sampling depth determine metabolome patterns.