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A geochemical and micropaleontological study of the Waipawa Formation in New Zealand was undertaken to investigate its depositional setting and possible relationship to major changes in the marine environment. The organic-rich formation was deposited in the Late Paleocene, during a third-order, eustatic sea-level rise. Precise age control is lacking, but deposition can be placed between a climatic cooling at 59.1 Ma and a thermal maximum at 55.5 Ma, during the transition from cold to warm-saline deep-water circulation in the South Pacific. Deposition occurred around most of the land mass, generally near the shelf break, and microfaunal evidence suggests dysaerobic conditions. There appears to have been no contemporaneous organic-rich sedimentation on the shelf, so the widespread high phytoplanktonic productivity, which is reflected in positive excursions in kerogen δ13C to −20‰, was probably caused by regional upwelling. However, the paleodistribution of the formation cannot be readily accounted for by wind-driven upwelling alone. There is strong positive correlation between organic content, kerogen δ13C values and unusually high abundance of 24-n-propylcholestanes (20–55% of C27–C30 regular steranes). Surface-water conditions favoured a particular group of phytoplankton that preferentially synthesised the precursor C30 sterols, and there is microfaunal evidence for warming. Carbonate oxygen isotopic data are also consistent with warming, but may be affected by diagenetic alteration. The Waipawa Formation may result from regional upwelling of warm, saline, oxygen-depleted, nutrient-rich deep water, in what appears to be an earlier and longer-term, but geographically more restricted, event than that responsible for the benthonic extinction event at 55.5 Ma.