Changing geography of Pukaki Lagoon over the last 8000 years. Diagram by Bruce Hayward.
Drilling in the floor of Pūkaki explosion crater has shown that, following the eruptions, the explosion crater (70 metres below present sea level) filled with fresh water and became a lake. No streams flowed into the lake and it periodically overflowed across the lowest part of the crater rim in the south. Little soil or sand washed into the lake either, and the main component of the sediment that slowly accumulated on its floor was the siliceous shells of diatoms (phytoplankton). Every so often, volcanic ash from a distant eruption landed in the lake and sank to form a distinctive layer on its floor. Coring of this sediment has revealed the presence of at least 14 black basaltic ash layers erupted from nearby Auckland volcanoes; 25 lighter grey, thin, andesitic ash layers erupted from Ruapehu, Tongariro and Taranaki volcanoes; and 16 cream to white, rhyolitic ash layers that were erupted from the Taupo and Okataina caldera volcanoes. Much of the 1.5-metre thickness of basaltic ash encountered at 56–58 metres beneath the surface was probably erupted from adjacent Crater Hill about 31,000 years ago. Fine scoria mantling the east side of Pūkaki tuff ring probably also came from Crater Hill fire-fountaining.
The lake sediment also contains abundant fossil pollen and spores which record the changing vegetation of the surrounding Manukau lowlands as the climate fluctuated between cool and warm, dry and wet, during the ups and downs of the Last Ice Age cycle. As sea level rose after the Last Ice Age it reached the height of the eroded overflow sill and the crater lake was breached about 8000 years ago. At the time, the lake was still about 30 metres deep and initially a deep saltwater lagoon was created. Every time the tide came in, it carried in suspended mud from the Manukau tidal flats. Inside Pūkaki Lagoon the suspended mud sank out of suspension and the lagoon rapidly filled up with 25 metres of marine mud. By 6000 years ago, Pūkaki had become entirely tidal mud flats which gradually accumulated more sediment that became colonised by salt marsh and mangroves around the fringes.