Polygonal faults, mainly oriented N50, N110 and N170, are abundant in the upper part of the mud-dominated Kai Formation (upper Miocene–lower Pliocene) of the Vøring Basin. A second, less-developed tier of polygonal faults, oriented N20, N80 and N140, exists at the base of the overlying Naust Formation (upper Pliocene–Present). The faults abruptly terminate upward below a thick interval of debris flows. We propose a dynamic model in which: (1) the development of polygonal faults discontinues temporarily as a result of a change in regional sedimentation, leading to inactive polygonal faults; (2) rapid emplacement of debris flows in the late Pleistocene creates a new interval of polygonal faults in the lower part of the Naust Formation immediately beneath the debris flow and some faults penetrate into the underlying Kai Formation; (3) some polygonal faults within the Kai Formation are reactivated and propagated upward into the base of the Naust Formation. The high interconnectivity between faulted layers allows the fluids to reach shallower depths, forming well-expressed pipes and pockmarks on the sea floor. The model of cessation/reactivation of polygonal faults constrains the sealing capacity of sedimentary cover over the reservoirs and helps to reconstruct the fluid migration history through the sedimentary column.