The Azolla event occurred in the middle Eocene period, around , when blooms of the freshwater fern Azolla occurred in the Arctic Ocean. As they sank to the stagnant sea floor, they were incorporated into the sediment; the resulting draw down of carbon dioxide from the atmosphere helped transform the planet from a "greenhouse Earth" state, hot enough for turtles and palm trees to prosper at the poles, to the icehouse Earth it has been since.
In sedimentary layers throughout the Arctic basin, a unit reaching at least 8 m in thickness is discernible. This unit consists of alternating layers; siliceous clastic layers representing the background sedimentation of planktonic organisms, usual to marine sediments, switch with millimetre-thick laminations comprising fossilised Azolla matter. This organic matter can also be detected in the form of a gamma radiation spike, that has been noted throughout the Arctic basin, making the event a useful aid in lining up cores drilled at different locations. Palynological controls and calibration with the high-resolution geomagnetic reversal record allows the duration of the event to be estimated at 800,000 years. The event coincides precisely with a catastrophic decline in carbon dioxide levels, which fell from 3500 ppm in the early Eocene to 650 ppm during this event.
During the early Eocene, the continental configuration was such that the Arctic sea was almost entirely cut off from the wider oceans. This meant that mixing — provided today by deep water currents such as the Gulf Stream — did not occur, leading to a stratified water column resembling today's Black Sea. High temperatures and winds led to high evaporation, increasing the density of the ocean, and — through an increase in rainfall — high discharge from rivers which fed the basin. This low-density freshwater formed a nepheloid layer, floating on the surface of the dense sea. Even a few centimetres of fresh water would be enough to allow the colonisation of Azolla; further, this river water would be rich in minerals such as phosphorus, which it would accumulate from mud and rocks it interacted with as it crossed the continents. To further aid the growth of the plant, concentrations of carbon (in the form of carbon dioxide) and accessible nitrogen in the atmosphere are known to have been high at this time.
Blooms alone are not enough to have any geological impact; to permanently draw down CO2 and cause climate change, the carbon must be sequestered, by the plants being buried and eventually fossilised. The anoxic bottom of the Arctic basin, a result of the stratified water column, permitted just this: the anoxic environment inhibits the activity of decomposing organisms and allows the plants to sit unrotted until they are buried by sediment and incorporated into the fossil record.
With 800,000 years of Azolla bloom episodes and a 4,000,000 km² basin to cover, even by very conservative estimates more than enough carbon could be sequestered by plant burial to account for the observed 80% drop in CO2 by this one phenomenon alone. This drop initiated a global temperature decline which continued for millions of years; the Arctic cooled from an average sea-surface temperature of 13 °C to today's −9 °C, and the rest of the globe underwent a similar change. For perhaps the first time in its history, the planet had ice caps at both of its poles. A geologically rapid decrease in temperature between 49 and , around the Azolla event, is evident: dropstones — which are taken as evidence for the presence of glaciers — are common in Arctic sediments thereafter. This is set against a backdrop of gradual, long-term cooling: It is not until that evidence for widespread polar freezing is common.