A high resolution chronology of deep water charophyte algal remains in the Pyramid Valley lake deposit, North Canterbury, South Island, New Zealand, records the presence and drainage of a previously unsuspected much larger (c. 50 ha) lake. The larger lake occupied the surrounding basin and the present lake (1 ha) was a semi-isolated embayment at its south-western margin. Fluctuating lake levels and its final drainage drove changes in the vegetation and hence in the habitats available for the avifauna recorded in the rich fossil record. A high precision radiocarbon age on the only South Island goose (Cnemiornis calcitrans) in the fauna coincided with the presence of lowland forest and not with the brief period when sedges and grassland colonised the newly exposed former lake bed. This suggests that the South Island goose was able to survive in different habitats through successive glacial-interglacial vegetation cycles. Information from other disciplines can be essential to interpreting both a fossil site and the circumstances surrounding the presence of a particular species in it.