Abstract A well-developed multi-tier polygonal fault system is located in the Great South Basin offshore New Zealand’s South Island. The system has been characterised using a high-quality three-dimensional seismic survey tied to available exploration boreholes using regional two-dimensional seismic data. In this study area, two polygonal fault intervals are identified and analysed, Tier 1 and Tier 2. Tier 1 coincides with the Tucker Cove Formation (Late Eocene) with small polygonal faults. Tier 2 is restricted to the Paleocene-to-Late Eocene interval with a great number of large faults. In map view, polygonal fault cells are outlined by a series of conjugate pairs of normal faults. The polygonal faults are demonstrated to be controlled by depositional facies, specifically offshore bathyal deposits characterised by fine-grained clays, marls and muds. Fault throw analysis is used to understand the propagation history of the polygonal faults in this area. Tier 1 and Tier 2 initiate at about Late Eocene and Early Eocene, respectively, based on their maximum fault throws. A set of three-dimensional fault throw images within Tier 2 shows that maximum fault throws of the inner polygonal fault cell occurs at the same age, while the outer polygonal fault cell exhibits maximum fault throws at shallower levels of different ages. The polygonal fault systems are believed to be related to the dewatering of sedimentary formation during the diagenesis process. Interpretation of the polygonal fault in this area is useful in assessing the migration pathway and seal ability of the Eocene mudstone sequence in the Great South Basin.