A continuous, 1,420-cm sediment record from Lake Pupuke, Auckland, New Zealand (37°S) was analysed for diatom taxonomy, concentration and flux. A New Zealand freshwater diatom transfer function was applied to infer past pH, electrical conductivity, dissolved reactive phosphorus and chlorophyll a. A precise, mixed-effect regression model of age versus depth was constructed from 11 tephra and 13 radiocarbon dates, with a basal age of 48.2 cal kyr BP. Diatom-inferred changes in paleolimnology and climate corroborate earlier inferences from geochemical analyses (Stephens et al. 2012), with respect to the timing of marked climate changes in the Last Glacial Coldest Phase (LGCP; 28.8-18.0 cal kyr BP), the Last Glacial Interglacial Transition (LGIT; 18.0 to ca. 12-10 cal kyr BP) and the Holocene, the onset of which is difficult to discern from LGIT amelioration, but which includes an early climatic optimum (10.2-8.0 cal kyr BP). The LGCP is readily defined by a reduction in lake level and effective precipitation, whereas the LGIT represents a period of rising lake level, with greater biomass during the Holocene. There was limited change in diatom assemblage structure, influx or inferred water quality during a Late Glacial Reversal (LGR; 14.5-13.8 cal kyr BP), associated with heightened erosional influx. In contrast, an LGIT peak in paleoproductivity is recorded by increased diatom influx from 13.8 to 12.8 cal kyr BP. Changes in sediment influx and biomass record complex millennial-scale events attuned to the Antarctic Cold Reversal (ACR; 14.5-12.8 cal kyr BP). Additional millennial-scale environmental change is apparent in the Holocene, with marked changes in lake circulation beginning at 7.6 cal kyr BP, including the onset of seasonal thermal stratification and rapid species turnover at 5.7 cal kyr BP. The most rapid diatom community turnover accompanied widely varying nutrient availability and greater seasonality during the last 3.3 cal kyr. Rising seasonality appears to have been linked to strengthened Southern Westerlies at their northern margins during the middle and late Holocene.