The Oligocene is a time of maximum submersion of the Zealandia landmass; it coincides with changes in oceanographic currents as well as with the inception of the Cenozoic plate boundary through New Zealand. Our analysis of offshore wells and seismic reflection lines in the Canterbury Basin reveals condensed Oligocene strata (<150 m thick), which were eroded by mid-Oligocene (~32–29 Ma) channels 1–10 km wide, 15–90 km long and up to ~200 milliseconds two-way-time deep. Onshore, we mapped corridors of complete erosion of the early Oligocene Amuri Limestone, overlain by younger Oligocene and Miocene strata using measured sections from the published literature. The synchronicity, similar trends, and comparable morphology of onshore and offshore channels suggest that they may have formed part of the same erosive system. We propose that a sea-level fall at ~32 Ma initiated the development of this drainage system with erosive channels converging towards canyons in the deeper water offshore. The drainage was active for up to 17 Ma, flowing primarily towards the south-east into the present-day Bounty Trough. The temporal (millions of years) and the spatial (hundreds of metres) scales of the sea-level fall are larger than would be expected for eustatic processes and we suggest that regional tectonic uplift played an important role in channel formation. The channel orientations and their eastward gradients, together with the Oligocene sedimentary facies observed in outcrop, suggest that the axis of uplift (and maximum topography) was primarily west of the Canterbury Basin. Tectonic shortening that collectively affected the western North Island – Marlborough Sounds – western Canterbury – western Otago regions may have produced uplift and eastward flowing early Oligocene channels in the Canterbury Basin. We observe that the orientations, geometries, and locations of early Oligocene drainage are similar to present day systems, suggesting they persisted as physiographic entities for at least 30 Myr, throughout Late Cenozoic plate tectonic deformation.