Animals can have structural, biogeochemical, and trophic legacy effects in streams and rivers that persist beyond the animal’s active presence in the ecosystem. These effects can be lost with the decline or disappearance of native fauna. Anthropogenic animal populations, such as livestock, may partially replace these legacy effects, although they often have important functional differences. In East Africa, large wildlife still persist at sufficient densities that they play an important role in shaping river ecosystems. Hippos alter riparian connectivity as they move between terrestrial feeding grounds and aquatic resting grounds, transporting a large magnitude of carbon and nutrients into the river that alters aquatic food web structure and ecosystem function. Wildebeest experience mass drownings during annual river crossings that contribute large amounts of carcass biomass that may decompose over decades. In some portions of the region, livestock are beginning to replace native wildlife on the landscape, and they also contribute terrestrial subsidies to aquatic systems during river crossings and watering. However, these subsidies differ in form and function from those of large wildlife. Conserving the ecological functions of animal legacies requires conservation of native animal species on the landscape.