Streams throughout the tropics have been altered by water diversion, channel modification, introduced species, and water quality degradation. The Hawaiian Islands, with watersheds ranging from the relatively pristine to the highly degraded, offer an opportunity to examine the impacts of human disturbance on native stream communities. For example, urbanization is often accompanied by stream-channel modification and reduced canopy cover, resulting in higher water temperatures and greater fluctuations in daily temperature. Even in relatively pristine watersheds, stream diversions can result in decreased flow velocity and water depth, reducing habitat availability. Dewatering of stream reaches can also inhibit downstream dispersal of larvae and upstream migration of juveniles and adults of native species. Many nonnative aquatic species are better adapted than native species to degraded habitats; once established in these habitats, they can cause further reduction in native populations through competition, predation, and the introduction of parasites or diseases. Understanding the relationship between habitat alteration and aquatic community structure is critical for developing sound management strategies.