In sub-Saharan Africa, many rivers are ephemeral and experience reduced hydrological flow during the dry season. The duration and intensity of these reductions in flow have been exacerbated regionally by increases in water abstraction and other anthropogenic modifications of watersheds and will be further intensified by climate change. Reduction in water availability is likely to have profound effects on the behaviour and spatial distribution of the common hippopotamus (Hippopotamus amphibius). H. amphibius is an ecologically important species because it transits between aquatic and terrestrial ecosystems and is a substantial vector of terrestrial subsidies into aquatic systems, thereby potentially promoting abundance and diversity of aquatic life. We hypothesized that in fact this role will be reversed during periods of extreme low flow and that nutrient overloading will negatively influence aquatic biodiversity. We explored effects of nutrient loading by H. amphibius on a historically perennial river in central Tanzania that, as a result of human modification, dries down seasonally into a series of isolated physically and hydrologically similar pools that host a wide range of densities of H. amphibius. Temporal patterns of abundance of H. amphibius as well as the chemical and biological aspects of the river ecosystem were assessed over a six-month period. GPS-collared H. amphibius yielded data on movement patterns of individuals as they responded to reduced flow and revealed the spatial scale over which H. amphibius impact the aquatic environment.