The northern ice cap formed about 2.4 Ma, resulting in a very arid phase in Australia. At this time Australia had only remnants of the closed canopy rainforests it had at the time it separated from Gondwana. The remnant forests were in places where the conditions were unchanged or had migrated into suitable areas that emerged as the climate changed during the Tertiary, as the continent dried out. The present day distribution of these remnant forests and fossil evidence indicates that the positions of the refugia didn't change during the Quaternary Period. The boundaries of these refugia, and the ecosystems contained within them, have changed over time, expanding and contracting with the changes of climate during the Pleistocene and Holocene.
The last Glacial Maximum (LGM) occurred between 25-16 thousand years BP. There is strong evidence that humans had occupied Australia 50,000 aBP. Thus people lived in Australia through a time when temperatures were about 3 K lower than now, winds were stronger, and the southern half of the continent wetter, especially over higher terrain. Also, the sea was some 130-150 m lower so that Tasmania was part of the mainland. Small glaciers were present in the Snowy Mountains and the Tasmanian highlands.
Analysis of buried pollen shows that there was a warming by several degrees and also an increase of rainfall from the depth of the last glaciation at 17 ka BP until the start of the Holocene. The major glaciers of New Zealand shrank to their minimum lengths shortly after 10,000 BP, while the steppe grassland and open savannah woodland of south-east Australia became replaced by forest. In Papua New Guinea's Highlands samples of organic matter, dated at 16,000 and 18,000 years BP, show a reduced rate of weathering, which would indicate temperatures 9.7 K and 11.3 K respectively lower than obtain now. Also, pollen from this area indicate minimum temperatures some 10 K lower than now, at about 18,000 BP, the time of the last cold phase of the Quaternary Ice Age. A drop of 6 K is suggested by evidence of former ice caps and glaciers on the highest peaks of Papua and Irian Jaya. Maximum rainfall in Australia was eventually reached at about 4000 BP in Tasmania and 8000 BP further north, in Queensland. Temperatures were highest, and about the same as today, between 8,000-6,000 BP. But maximum Holocene temperatures in New Zealand (about 2 K warmer than nowadays) occurred about 9000 BP. So the time of greatest warmth was not reached uniformly in the region. Over 10,000 years humans had to adjust to a climate change whose extent exceeded what is reckoned on in contemplating the future effect of doubling atmospheric carbon dioxide. On the other hand, it is unlikely that post-LGM warming exceeded a rate of 0.1 K/century in Australia, which is but a tenth of current global warming.
Overall, Australian forests and woodlands became much more restricted during glacial times, grasslands replacing many of them. For much of the continent, this was not the result of the land being in the grip of sub-alpine conditions. The continent lay in mid latitudes, with very little high ground, so the temperatures during the Ice Age didn't drop too drastically. The great expansion of grasslands, and changes in ecosystems that appeared as though they were the result of extreme cold, were actually more likely to be the result of seasonal aridity, with accompanying high winds and increased evaporation, and to the increased fires that accompanied the drying out near the glacial peaks.
By 2.4 Ma many dryland vegetation types had been established. In places where topography, soil type and salinity produced extreme aridity, drought-adapted plants had already been selected, pre-adapting them to fill the niches that increasingly became available as aridity spread over the land. During the glacials and interglacials, the time scale were changing from millions of years to thousands of years. As the dry times came and went, as the glacial climate fluctuated, stopping increased aridity in some parts and slowing its spread in others, the boundaries of the various vegetation types expanded and contracted in sync with the climate.
In the southern, warm temperate parts of the continent the climate was settling on a pattern of wet winters and dry summers. The northern section was becoming subject to the tropical monsoonal belt, with wet summers and dry winters. In between, the climate was becoming close to one long dry season that lasted the whole year, the water that arrived was down the streams from the northern monsoonal regions. Tasmania and the highlands in the south-east of the continent had a cool temperate climate. During glacial stages, as well as increased aridness, there were increases in wind speed, fewer cyclones in the north, more wind-blown sand and cooler air and oceans, and snow and ice in Tasmania and Mt Kosciusko.
The sea level rose in the interglacials and fell during the glacials, so that the amount of change depended on the severity of the stages of the glaciation. The cyclical onslaught of the aridity produced by the sequence of glacial periods gradually converted more of Australia to desert. Each glacial period added more of the continent to the zone of permanent desert, and after each dry period more of the land was unable to return to its previous state. Fire became an increasing factor as the drying progressed. Looked at as a whole, over the period of the last 2.4 million years, it seems Australia has been becoming more arid, even from the beginning of the Ice Age 15 Ma. The drying process was lifted a notch with the arrival of the first Australians about 60,000 years ago, and up a further notch with the arrival of the new Australians 200 years ago.
It was during the last 1.6 million years that the climate patterns and variability of Australia gradually became established to what they are today. Over large areas of southern and inland Australia are deeply weathered profiles of Early Pliocene age, acidic and often cemented with iron to form duricrust, that are often overlain by sediments rich in calcium and alkaline soils. Wind transport is the agency for deposition of these fine-grained deposits. Sedimentation had been occurring in shallow lakes in Central Australia throughout the Miocene and the Early Pliocene. The Etadunna Formation and Namba formation, among others, are examples of these sediments. These lake sediments are often capped by clay layers. The arid, windy times when the lakes were dry are evidenced by the fine, wind-blown material that was blowing, deflating, from the dry lake beds, the continual evaporation of the water concentrating their mineral continent, the water becoming progressively more saline and gypsum-rich. The sedimentation regime changes in the Upper Tirari Formation where a gypsum-cemented layer occurs above the Etadunna formation. The start of desertification is marked by deposition of large scale aeolian deposits and the development of alkaline soils in the Late Pliocene. It appears 2.4 Ma was also the time when this large-scale change occurred.
The effects of sea level fluctuations that occurred as the glacials and interglacials waxed and waned had a big effect on the Australian coastline. At times of high sea level, large areas of the continental margins were covered and marine deposits laid down. One result of these high sea levels, during interglacials, is the presence of dune strand lines and shell beds in places far inland from the present coast. The continental shelves were exposed in many places at times of low-sea-level glacials. At these drier times coastal rivers cut deep channels through the deposits laid down during the times of high sea level. These drowned river valleys form the coastline of present-day Australia.
During glacial times, when the continental shelf was exposed, the sand that had been the ocean floor was blown inland in the windy, dry conditions. The sand formed dunes that were often blown into sand sheets. This process formed the Western Australian coastal strip, the onshore section of the Perth Basin. This coastal belt has been relatively stable. Events occurring in the Late Pliocene to Pleistocene have mostly been preserved. Near Perth, in the central section of the basin, marine sequences from the Pliocene to the Quaternary, there are deposits parallel to the present coastline, bounded to the east by the Darling Fault. This fault separates the Perth Basin from the Yilgarn Block, the edges of which form the Darling Scarp. These marine sequences increase in elevation and age towards the scarp, representing different stages in the Pleistocene. During the Pleistocene, uplift of the Basin and the Yilgarn Plateau occurred, raising the various deposits to higher elevations, and in the same period, the crustal shelf margin was subsiding. A complex of sediments deposited at ancient shorelines, the Yoganup Formation and Ascot Formation, and the Bassendean Sand, on the inner shelves, and dunes. The Pliocene-Pleistocene units comprising the Ascot Formation, are sub-surface, forming one of the water-mound aquifers that Perth depends on for its water supply. These are quartzite sands.
About 1.5 million years ago, central Victoria enjoyed high summer rainfall, and was home to vast temperate rainforests, similar to those further north in New South Wales and Queensland today. New research now shows the region had a spectacularly diverse sclerophyll flora – tough-leaved, woody plants – such as eucalypts, acacias and banksias. The richness was equivalent to the richness of sclerophyll vegetation found today in south-west Western Australia, and in the Cape region of South Africa, which are some of the most diverse communities of plants on the planet. The findings indicate that over the past million years, as Australia's climate underwent a series of ice ages and became drier and more variable, many plants were wiped out. Dr Kale Sniderman and his research partner Dr Greg Jordan, from the University of Tasmania, extracted fossil leaves from 1.5 million-year-old sediments at the bottom of a lake near Daylesford, Victoria. Here, they found 69 now-extinct sclerophyll species. Sniderman and Jordan believe rapid climatic changes, which occurred as a result of successive ice ages, are responsible for Victoria's biodiversity loss. When climate shifts from ice age to interglacial, or vice versa, the species may be confronted suddenly by a very different environment.
The plant fossil record of the Late Pliocene and Early Pleistocene is fragmentary. At this time there was rapid change. The sorting of the flora occurred as the area covered by forests decreased, being replaced by sclerophyll forests, which were becoming widespread. Aridity was tightening its grip on central Australia. The Ice Age began to make its presence felt in Tasmania, with large areas of glaciation occurring during the Ross Glaciation of the Late Pliocene and Early Pleistocene. Though the exact time of the beginning of this glaciation is unknown it it thought it may coincide with the sharp drop in global temperature 900,000 BP.
As a result of the continuation of the cooling trend, by 700,000 BP the polar ice caps had reached a new maximum. The Linda Glacial Stage in Tasmania has been dated to this time, about 730,000 BP. The deposits from this glacial stage are extremely weathered and overlain by those from later glaciations, so they are not well known. At Regatta Point on Macquarie Harbour, western Tasmania, macrofossils and pollen have been found that indicate a Late Pliocene to Pleistocene age for the deposit. The rainforest community was present, but it differed from the one that covered the area in the Oligocene at Pioneer. There was lower density and smaller leaf size in the younger rainforest, as well as lower diversity. In this rainforest there were Nothofagus cunninghamii, Eucryphia (leatherwood), Atherosperma mochatum (sassafras), Quintinis (possum wood), Acacia, Lagarostrobos franklinii (Huon pine), Athrotaxis seleginiodes (King Billy pine), A. cupressoides (pencil pine), Podocarpus, Tasmannia (Winteraceae) and the tree-fern Dicksonia antarctica. There was also a sclerophyll community, similar to the one that is there at the present, composed of Eucalyptus, Casuarina, Banksia, epacrids and tea trees.
The list of temperate rainforest plants from the Pliocene-Pleistocene differs very little from the species comprising the modern beech forests of Tasmania. In exception is Quintinia, which is now apparently extinct, though it remained a part of the Tasmanian rainforest at this location much longer than it did in the rainforests of the southern parts of the mainland. Daisies and grasses, as well as Acacia and Casuarina, are prominent members of the vegetation in the Latrobe Valley, Victoria, from the Pliocene-Pleistocene transition. This has been shown from pollen analysis. It is thought to indicate cool or dry conditions, or both. Generally, by the end of the Tertiary Period rainforest had contracted to the eastern edge of the continent, close to their present range. As the climate fluctuated during the Quaternary, the boundaries of the rainforest also fluctuated, expanding and contracting as the conditions became wetter then drier again.
Late Pliocene to Pleistocene fauna from the Murray-Darling Basin, when part of the region was occupied by Lake Bungunnia, is shown from fossils in the area. Among the fauna were dasyurids (native cats), wombats, potoroos, wallabies, kangaroos and rodents (placentals). There were 2 groups of rodents, one of which now occurs in arid regions. The other is a different kind that is only distantly related and is now extinct. Among the marsupials, the hare wallaby (Lagorchestes) survives at the present in arid parts of the country. This indicates that the fauna from the Pliocene-Pleistocene were already arid-adapted.
In younger deposits in the same area there are fish, turtles, Thylacoleo (marsupial lion), macropods (wallabies and kangaroos) of uncertain types, and Diprotodon. To the north, in the Menindee Lakes area there were Euowenia (a protodontia) and Protemnodon (giant kangaroo). The fossils here were found in bore holes. A lungfish tooth was found at Lake Tandou. This was the last known lungfish from southern Australia. They are now only found in the Mary River and Burnett River in Queensland. They seem to have disappeared from the southern parts of Australia after the drying out of Lake Bungunnia about 700,000 BP, long before the last major phase of aridity from 18000-15000 BP
The Kanunka Fauna from the Late Pliocene-Pleistocene, in stream channel deposits and the Katipiri Sands in the Lake Eyre Basin, display a diverse assemblage of animals—lungfish, chelid turtles, crocodiles, cormorants, flamingos, other water birds, hare wallabies and nail-tailed wallabies. There were large Diprotodontidae, Diprotodon, Zygomaturus and the giant goanna Megalania pricia. These sediments were palaeodrainage channels of Cooper Creek and the Warburton River. They merge into wind-blown dune sediments of the latest Pleistocene and Holocene. Fossils from the last glacial maximum occur in these sediments.
Among the fossils found in the Kanunka Fauna were two types of flamingo, one of which is now present in Africa, and another that is widespread in tropical and temperate regions. The reason for the local extinction of the now African flamingos is unclear. A suggested reason might have been competition from more adaptable filter-feeding ducks that can feed in varying water conditions, and possibly from other water birds. In the later stages of the Pleistocene the water levels were fluctuating as the shallow lakes repeatedly dried out, which would have made it a difficult time for specialist feeders that couldn't adapt to the varying conditions. Those adapted to a specific niche would have needed to adapt rapidly to other niches or die out. There must have been large amounts of shallow water in Australia between the Miocene and the later Pleistocene to support flamingos.
Among the species of the Malkuni Fauna, from the Katapuri Sands and from the lower Cooper, were lungfish, crayfish, turtles and crocodiles. There was a diverse bird fauna—grebes, pelicans, cormorants, rails, herons, a crane, ducks and spoonbills. The mammals included Sarcophilus (Tasmanian devils), brushtail possums and bettongs. Also among the mammals were extinct megafauna such as Sthenurus (browsing kangaroos), Phasocolonus (giant wombat), Protemnodon (a giant kangaroo), Procoptodon (giant browsing kangaroo), and two diprotodontids (Diprotodon and Zygomaturus). There must have been water present continuously prior to the drying because of the presence of lungfish and crocodiles; they became locally extinct as soon as the drying began.