Abstract Many varied and complex environmental problems, particularly row crop and grazing agriculture, urbanization, highway building, timber harvesting, and water projects such as dams, water withdrawals, and stream channel modifications have seriously affected the health of freshwater resources in many parts of the world. The health of aquatic resources can be measured in many ways. Among them, biotic (or biological) integrity is a concept most commonly used by the public, biologists, resource managers, and policy makers to measure the status of aquatic systems. Biotic integrity 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 natural habitat of the region.” Aquatic systems of high biotic integrity have a biological community in which composition, structure, and function have not been seriously altered by human activities. Such systems can withstand or rapidly recover from some perturbations imposed by natural environmental processes and survive many major disruptions induced by humans. Aquatic systems that lack integrity are often degraded and when further perturbed by natural or human‐induced events are likely to change rapidly to an even more undesirable status.