Abstract Fish habitat is composed of the physical, chemical, and biological features of the environment that allow fish to survive, grow, and reproduce. This may involve migration among different habitats as fishes complete portions of their life cycle. The destruction and degradation of fish habitat is one of the greatest threats to freshwater and marine fishes. Fish habitat stressors ultimately affect populations through processes acting on survival, growth, and reproduction. Fish habitat indicators and indices describe the suitability of an environment for fishes on the basis of physiological, behavioral, or ecological preferences. A number of modeling approaches have been used to determine the effects of habitat availability on fishes, including bioenergetic, matrix, individual‐based, trophodynamic, and ecosystem models. The geophysical and biological attributes of fish habitat, combined with both upstream and landscape effects, truly necessitates an ecosystem approach to the management of fish habitat.