Groundwater metabolome responds to recharge in fractured sedimentary strata

•Groundwater dissolved organic matter (DOM) connects microbial and geochemical spheres.•We demonstrate 5-years DOM (metabolomics) monitoring by mass spectrometry.•DOM-feature fingerprints are highly variable but converge periodically across sites.•An association of this convergence with discharge/recharge flows is evident.•DOM dynamics add insight to responses of groundwater to climatic events / extremes.