Biological integrity is associated with how "pristine" an environment is and its function relative to the potential or original state of an ecosystem before human alterations were imposed. Biological integrity is built on the assumption that a decline in the values of an ecosystem's functions are primarily caused by human activity or alterations. The more an environment and its original processes are altered, the less biological integrity it holds for the community as a whole. If these processes were to change over time naturally, without human influence, the integrity of the ecosystem would remain intact. The integrity of the ecosystem relies heavily on the processes that occur within it because those determine what organisms can inhabit an area and the complexities of their interactions.
The concept of biological integrity first appeared in the 1972 amendments to the U.S. Federal Water Pollution Control Act, also known as the Clean Water Act. The United States Environmental Protection Agency (EPA) had used the term as a way to gauge the standards to which water should be maintained, but the vocabulary instigated years of debate about the implications of not only the meaning of biological integrity, but also how it can be measured. The first conference about the term occurred in March 1975 called "The Integrity of Water" and provided the first accepted definition of biological integrity (see below). In 1981, EPA assembled a field of experts from the U.S. Fish and Wildlife Service, academia, and its own staff to further refine the definition and identify key indicators to quantitatively measure biological integrity. The conference not only identified a definition, but also methods to evaluate the community, and they established that multiple sites should be used to determine the condition of the environment
Today, the accepted definition is “the capability of supporting and maintaining a balanced, integrated, adaptive community of organisms having a species composition, diversity, and functional organization comparable to that of the natural habitat of the region.” This definition was adapted from Frey (1977). The implications of this definition are that living systems have a variety of scales relative to which they exist, that one can quantify the parts that sustain or contribute to a system's functioning and that all systems must be seen in the context of their environments and evolutionary history. This term primarily refers to aquatic environments because the vocabulary is derived from the Clean Water Act, but the concepts can be applied to other ecosystems.