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The ecosystem of a lake includes biotic (living) plants, animals and micro-organisms, as well as abiotic (nonliving) physical and chemical interactions.

Lake ecosystems are a prime examples of lentic ecosystems. Lentic refers to standing or relatively still water, from the Latin lentus, which means sluggish. Lentic waters range from ponds to lakes to wetlands, and much of this article applies to lentic ecosystems in general. Lentic ecosystems can be compared with lotic ecosystems, which involve flowing terrestrial waters such as rivers and streams. Together, these two fields form the more general study area of freshwater or aquatic ecology.

Lentic systems are diverse, ranging from a small, temporary rainwater pool a few inches deep to Lake Baikal, which has a maximum depth of 1740 m. The general distinction between pools/ponds and lakes is vague, but Brown states that ponds and pools have their entire bottom surfaces exposed to light, while lakes do not. In addition, some lakes become seasonally stratified (discussed in more detail below.) Ponds and pools have two regions: the pelagic open water zone, and the benthic zone, which comprises the bottom and shore regions. Since lakes have deep bottom regions not exposed to light, these systems have an additional zone, the profundal. These three areas can have very different abiotic conditions and, hence, host species that are specifically adapted to live there.

The natural environment encompasses all living and non-living things occurring naturally on Earth or some region thereof. It is an environment that encompasses the interaction of all living species. The concept of the natural environment can be distinguished by components:

The natural environment is contrasted with the built environment, which comprises the areas and components that are strongly influenced by humans. A geographical area is regarded as a natural environment.

It is difficult to find absolutely natural environments, and it is common that the naturalness varies in a continuum, from ideally 100% natural in one extreme to 0% natural in the other. More precisely, we can consider the different aspects or components of an environment, and see that their degree of naturalness is not uniform. If, for instance, we take an agricultural field, and consider the mineralogic composition and the structure of its soil, we will find that whereas the first is quite similar to that of an undisturbed forest soil, the structure is quite different.

Natural environment is often used as a synonym for habitat. For instance, when we say that the natural environment of giraffes is the savanna.

Water stagnation occurs when water stops flowing. Stagnant water can be a major environmental hazard.^{[citation needed]}

Anoxic waters are areas of sea water, fresh water or groundwater that are depleted of dissolved oxygen. This condition is generally found in areas that have restricted water exchange.

In most cases, oxygen is prevented from reaching the deeper levels by a physical barrier (e.g. mud) as well as by a pronounced density stratification, in which, for instance, heavier hypersaline waters rest at the bottom of a basin. Anoxic conditions will occur if the rate of oxidation of organic matter by bacteria is greater than the supply of dissolved oxygen.

Anoxic waters are a natural phenomenon, and have occurred throughout geological history. Anoxic basins exist at present, for example, in the Baltic Sea, and elsewhere (see below). Recently, there have been some indications that eutrophication has increased the extent of the anoxic areas in areas including the Baltic Sea, the Gulf of Mexico and Hood Canal in Washington State.

Biodiversity is the degree of variation of life forms within a given species, ecosystem, biome, or planet. Terrestrial biodiversity tends to be highest at low latitudes near the equator, which seems to be the result of the warm climate and high primary productivity. Marine biodiversity tends to be highest along coasts in the Western Pacific, where sea surface temperature is highest and in mid-latitudinal band in all oceans. Biodiversity generally tends to cluster in hotspots, and has been increasing through time but will be likely to slow in the future.

Rapid environmental changes typically cause mass extinctions. One estimate is that <1%-3% of the species that have existed on Earth are extant.

Since life began on Earth, five major mass extinctions and several minor events have led to large and sudden drops in biodiversity. The Phanerozoic eon (the last 540 million years) marked a rapid growth in biodiversity via the Cambrian explosion—a period during which the majority of multicellular phyla first appeared. The next 400 million years included repeated, massive biodiversity losses classified as mass extinction events. In the Carboniferous, rainforest collapse led to a great loss of plant and animal life. The Permian–Triassic extinction event, 251 million years ago, was the worst; vertebrate recovery took 30 million years. The most recent, the Cretaceous–Paleogene extinction event, occurred 65 million years ago and has often attracted more attention than others because it resulted in the extinction of the dinosaurs.