Australian tropical rivers are dependent on highly seasonal rainfall and runoff between November and April. They also transport low sediment and solute loads, except where catchments have been disturbed by mining, grazing and cropping. Aquatic habitats or channel units are the physical template influencing fish communities. Pools provide dry-season refuges for fish and channels provide pathways for movement between refuges when streamflows are re-established. A preliminary geomorphological typology of Australian tropical river reaches (excludes estuaries) is proposed that defines nine distinct river types: (1) bedrock rivers (upland channels and gorges); (2) bedrock-confined rivers; (3) avulsive rivers; (4) meandering rivers (confined meandering, laterally migrating unconfined and laterally stable unconfined); (5) straight rivers; (6) floodouts; (7) island- and ridge-anabranching rivers; (8) co-existent mud-braided and anabranching rivers; and (9) extensive freshwater wetlands and billabongs. Many of these have not been recognised overseas and are unique. Channel units differ greatly between river types and contribute to distinctive fish communities in different river types. As expected, fish diversity decreases upstream because of less diverse habitat and natural barriers to fish movement at steps, falls and turbulent cascades and rapids. Fish kills occur in most years and are caused by several different factors that reduce dissolved oxygen.