Estuarine habitats, and the fish assemblages associated with them, are potentially impacted upon by many anthropogenic influences which can have a direct influence on the food resources, distribution, diversity, breeding, abundance, growth, survival and behaviour of both resident and migrant fish species. The direct and indirect coupling between ichthyofaunal communities and human impacts on estuaries reinforces the choice of this taxonomic group as a biological indicator that can assist in the formulation of environmental and ecological quality objectives, and in the setting of environmental and ecological quality standards for these systems. This review examines the rationale and value of selecting fishes as bio‐indicators of human induced changes within estuaries, using examples from both the northern and southern hemispheres. The monitoring of estuarine ‘health’ using fish studies at the individual and community level is discussed, with an emphasis on the potential use of estuarine fishes and their monitoring and surveillance in national and international management programmes. In illustrating the above concept, examples are presented of the way in which fishes are threatened by anthropogenic impacts and of the way in which teleosts can contribute to a monitoring of estuarine ecosystem health.