We present the results of a multidisciplinary study on the relationships between the structural architecture of an extensional fault system in poorly lithified shallow marine sands and the associated pattern of diagenetic carbonate concretions. Based on their shape, spatial distribution, cement texture and chemistry, and isotopic signature, carbonate concretions are grouped into (1) tabular (encompassing also nodular and lens-shaped) concretions developed within the fault zones, and (2) elongate and coalescent strata-bound concretions formed adjacent and mostly parallel to fault zones. Cement chemistry and morphology, as well as stable carbon–oxygen isotopic signatures, indicate that tabular concretions formed during early diagenesis in the vadose mixing marine–meteoric zone, possibly during coseismic rupture propagation and, in the interseismic periods, as a result of slow capillary suction along the low-permeability fault zones. On the other hand, elongate concretions formed after regional uplift and during telodiagenesis by precipitation from meteoric, phreatic water flowing parallel to the fault zones, which acted as a hydraulic barrier. The concretion patterns record the evolution of fluid flow orientation and the changing chemistry of fault-zone fluids, which were fundamentally driven by fault system propagation and resulting fault architecture during two major diagenetic stages.