With an estimated 2,500 to 3,000 fish species, the Amazon basin is the largest biodiversity center of freshwater fishes. The large number is related to the size of the basin, a large habitat diversity, high speciation rates of different groups, and low extinction rates resulting from a rather stable tropical climate which has persisted over long geological periods. Amazonia is characterized by a very dense network of streams and rivers, connected to extended floodplains and wetland areas. There are only a few small permanently isolated deep lakes in the area. Rapids and waterfalls along the border of the Guyana shield, the Central Brazilian shield and the Andes separate the downstream and upstream fish faunas of major rivers. Estimates indicate that about half of the fish fauna colonizes the large river floodplain systems along the lower and middle reaches of the rivers and the other half the headwater streams. Knowledge about fish habitats is concentrated mostly on large river floodplains near large cities, which provide infrastructure for research, and habitat conditions in large areas are virtually unknown. Information is scattered in limnological, botanical, geographical, and aquarium literature. Ongoing research concentrates mostly on the inland fisheries.
Large parts of the Amazon River basin are still in pristine condition as are the fish habitats. However, human activities, including the transformation of large savanna and rain forest areas into agricultural land, the construction of large reservoirs for hydroelectric power generation, and mining profoundly modify fish habitats, and threaten species diversity mainly in small streams. Environmental legislation for the protection of streamside vegetation is sometimes contradictory and often not respected by the landowners. In the long run, specific fish communities and their habitats will only be fully protected in national parks and other protected areas. Even these areas suffer illegal human activities because of insufficient administration. There is an urgent need for the classification of fish habitats throughout the basin and the proposal of specific protection measures.