A paired (black and white) layer of the varved lake sediments corresponds to a year. During winter, when organisms die, carbon is deposited, resulting in a black layer. In the same year, during summer, only a few organic materials are deposited, resulting in a white layer on the lake bed. These are commonly used to track past paleontological events.

Natural lakes provide a microcosm of living and nonliving elements that are relatively independent of their surrounding environment. Therefore, lake organisms can often be studied in isolation from the lake's surroundings.

Limnology is the study of inland waters - lakes (both freshwater and saline), reservoirs, rivers, streams, wetlands, and groundwater - as ecological systems interacting with their drainage basins and the atmosphere.

Lake ecosystem, and Lake aeration

Lake Billy Chinook, Deschutes National Forest, Oregon

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Lake Cügün, Kırşehir, Turkey

Lake of Flowers (Liqeni I Lulëve), one of the Lurë Mountains glacial lakes, Albania

Limnology divides lakes into three zones:

i.The littoral zone, a sloped area close to land;

ii.The photic or open-water zone, where sunlight is abundant;

iii.The deep-water profundal or benthic zone, where little sunlight can reach.

The depth to which light can reach in lakes depends on turbidity, determined by the density and size of suspended particles. A particle is in suspension if its weight is less than the random turbidity forces acting upon it. These particles can be sedimentary or biological in origin and are responsible for the color of the water. Decaying plant matter, for instance, may be responsible for a yellow or brown color, while algae may cause greenish water. In very shallow water bodies, iron oxides make water reddish-brown. Biological particles include algae and detritus. Bottom-dwelling detritivorous fish can be responsible for turbid waters because they stir the mud in search of food. Piscivorous fish contribute to turbidity by eating plant-eating (planktivorous) fish, thus increasing the number of algae. The light depth or transparency is measured by using a Secchi disk, a 20-cm (8 in) disk with alternating white and black quadrants. The depth at which the disk is no longer visible is the Secchi depth, a measure of transparency. The Secchi disk is commonly used to test for eutrophication. For a detailed look at these processes.

A lake moderates the surrounding region's temperature and climate because water has a very high specific heat capacity. In the daytime, a lake can cool the land beside it with local winds, resulting in a sea breeze; in the night it can warm it with a land breeze.

How do lakes disappear?

The satellite image of Lake Chad in 2001 showed the actual lake in blue, and vegetation on top of the old lake bed in green.

Badwater Basin dry lake, February 15, 2007.

The lake may be infilled with deposited sediment and gradually become a wetland such as a swamp or a 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 resulting in a dynamic equilibrium between marsh and lake. This is significant since wildfire has been largely suppressed in the developed world over the past century. This has artificially converted many shallow lakes into emergent marshes. 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 some animals. 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, ephemeral lakes, or seasonal lakes and can be found in karstic terrain. A prime example of an intermittent lake is Lake Cerknica in Slovenia or Lag Prau Pulte in Graubünden. Other intermittent lakes are only the result of above-average precipitation in a closed, or endorheic basin, usually filling dry lake beds. This can occur in some of the driest places on earth, like Death Valley. This occurred in the spring of 2005, after unusually heavy rains. The lake did not last into the summer and was quickly evaporated. A more commonly filled lake of this type is Sevier Lake of west-central Utah.

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 s.h.i.+ft 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.

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.

Extraterrestrial lakes

t.i.tan's north polar hydrocarbon seas and lakes as seen in a false-color Ca.s.sini synthetic aperture radar mosaic. Only one world other than Earth is known to harbor large lakes, Saturn's largest moon, t.i.tan. Photographs and spectroscopic a.n.a.lysis by the Ca.s.sini–Huygens s.p.a.cecraft show liquid ethane on the surface, which is thought to be mixed with liquid methane. The largest t.i.tanean lake, Kraken Mare at 400,000 km, is three times the size of any lake on Earth, and even the second, Ligeia Mare, is estimated to be slightly larger than Earth's Lake Michigan–Huron.