An ecosystem is a community plus the physical environment that it occupies at a given time. An ecosystem can exist at any scale, for example, from the size of a small tide pool up to the size of the entire biosphere. However, lakes, marshes, and forest stands represent more typical examples of the areas that are compared in discussions of ecosystem diversity.

Broadly speaking, the diversity of an ecosystem is dependent on the physical characteristics of the environment, the diversity of species present, and the interactions that the species have with each other and with the environment. Therefore, the functional complexity of an ecosystem can be expected to increase with the number and taxonomic diversity of the species present, and the vertical and horizontal complexity of the physical environment. However, one should note that some ecosystems (such as submarine black smokers, or hot springs) that do not appear to be physically complex, and that are not especially rich in species, may be considered to be functionally complex. This is because they include species that have remarkable biochemical specializations for surviving in the harsh environment and obtaining their energy from inorganic chemical sources (e.g., see discussions of Rothschild and Mancinelli, 2001 [link]).

The physical characteristics of an environment that affect ecosystem diversity are themselves quite complex (as previously noted for community diversity). These characteristics include, for example, the temperature, precipitation, and topography of the ecosystem. Therefore, there is a general trend for warm tropical ecosystems to be richer in species than cold temperate ecosystems (see "Spatial gradients in biodiversity"). Also, the energy flux in the environment can significantly affect the ecosystem. An exposed coastline with high wave energy will have a considerably different type of ecosystem than a low-energy environment such as a sheltered salt marsh. Similarly, an exposed hilltop or mountainside is likely to have stunted vegetation and low species diversity compared to more prolific vegetation and high species diversity in sheltered valleys (see Walter, 1985 [link], and Smith, 1990 [link] for general discussions on factors affecting ecosystems, and comparative ecosystem ecology).

Environmental disturbance on a variety of temporal and spatial scales can affect the species richness and, consequently, the diversity of an ecosystem. For example, river systems in the North Island of New Zealand have been affected by volcanic disturbance several times over the last 25,000 years. Ash-laden floods running down the rivers would have extirpated most of the fish fauna in the rivers, and recolonization has been possible only by a limited number of diadromous species (i.e., species, like eels and salmons, that migrate between freshwater and seawater at fixed times during their life cycle). Once the disturbed rivers had recovered, the diadromous species would have been able to recolonize the rivers by dispersal through the sea from other unaffected rivers (McDowall, 1996 [link]).

Nevertheless, moderate levels of occasional disturbance can also increase the species richness of an ecosystem by creating spatial heterogeneity in the ecosystem, and also by preventing certain species from dominating the ecosystem. (See the module on Organizing Principles of the Natural World for further discussion).

Ecosystems may be classified according to the dominant type of environment, or dominant type of species present; for example, a salt marsh ecosystem, a rocky shore intertidal ecosystem, a mangrove swamp ecosystem. Because temperature is an important aspect in shaping ecosystem diversity, it is also used in ecosystem classification (e.g., cold winter deserts, versus warm deserts) (Udvardy, 1975 [link]).

While the physical characteristics of an area will significantly influence the diversity of the species within a community, the organisms can also modify the physical characteristics of the ecosystem. For example, stony corals (Scleractinia) are responsible for building the extensive calcareous structures that are the basis for coral reef ecosystems that can extend thousands of kilometers (e.g. Great Barrier Reef). There are less extensive ways in which organisms can modify their ecosystems. For example, trees can modify the microclimate and the structure and chemical composition of the soil around them. For discussion of the geomorphic influences of various invertebrates and vertebrates see (Butler, 1995 [link]) and, for further discussion of ecosystem diversity see the module on Processes and functions of ecological systems .