A lake may be in-filled with deposited sediment and gradually become a wetland such as a swamp or marsh. Large water plants, typically reeds, accelerate this closing process significantly because they partially decompose to form peat soils that fill the shallows. Conversely, peat soils in a marsh can naturally burn and reverse this process to recreate a shallow lake. Turbid lakes and lakes with many plant-eating fish tend to disappear more slowly. A "disappearing" lake (barely noticeable on a human timescale) typically has extensive plant mats at the water's edge. These become a new habitat for other plants, like peat moss when conditions are right, and animals, many of which are very rare. Gradually the lake closes, and young peat may form, forming a fen. In lowland river valleys, where a river can meander, the presence of peat is explained by the infilling of historical oxbow lakes. In the very last stages of succession, trees can grow in, eventually turning the wetland into a forest.

Some lakes can disappear seasonally. These are called intermittent lakes and are typically found in karstic ( an area full of underground caves)terrain.

Sometimes a lake will disappear quickly. On 3 June 2005, in Nizhny Novgorod Oblast, Russia, a lake called Lake Beloye vanished in a matter of minutes. News sources reported that government officials theorized that this strange phenomenon may have been caused by a shift in the soil underneath the lake that allowed its water to drain through channels leading to the Oka River.

The presence of ground permafrost is important to the persistence of some lakes. According to research published in the journal Science ("Disappearing Arctic Lakes," June 2005), thawing permafrost may explain the shrinking or disappearance of hundreds of large Arctic lakes across western Siberia. The idea here is that rising air and soil temperatures thaw permafrost, allowing the lakes to drain away into the ground.

Neusiedler See, located in Austria and Hungary, has dried up many times over the millennia. As of 2005, it is again rapidly losing water, giving rise to the fear that it will be completely dry by 2010.

Some lakes disappear because of human development factors. The shrinking Aral Sea is described as being "murdered" by the diversion for irrigation of the rivers feeding it