Extensive geophysical surveying of western Lake Superior has revealed the presence of a system of small extensional faults deforming a 10–15-m-thick interval of glacio-lacustrine clays of early Holocene age over an area of ∼5000 km2. Mapping of these closely spaced faults shows that they have (1) a polygonal planform geometry with a large range of strikes and (2) oblique to orthogonal intersection geometries. The fault system is layer bound and restricted to fine-grained postglacial sediments. The fault system is overlain by an extensive field of 100–400-m-diameter, 1–7-m-deep pockmarks, directly implicating the faults in the process of pockmark formation. The fault system is the youngest and most accurately dated example of a polygonal fault system described to date and the first to be described from a freshwater setting. This example conclusively demonstrates that nontectonic faulting can occur in sediment buried only a few meters and can be accompanied by highly focused fluid flow, a result that has wide implications for compaction processes of fine-grained sediments.