Hippos transfer massive quantities of trophic resources from terrestrial to aquatic ecosystems through defecation. The ramifications of the latter for the functioning of benthic ecosystems are unknown, but are dependent ultimately on rates of utilisation relative to inputs. Low input and high utilisation can strengthen bottom-up pathways and enhance consumer biomass and abundance. However, if inputs exceed utilisation rates, dung can accumulate, leading to a decline in water quality, with important repercussions for resident assemblages. Here, we quantify the consequences of hippo dung inputs on benthic assemblages in an estuarine lake in South Africa. The system supports over a thousand hippos, and during recent drought periods (extending over a decade), hippo dung has been observed to form mats over benthic habitats. Enrichment of plots using exclusion/inclusion cages with dung at naturally occurring concentrations indicated a decline in benthic chl-a by roughly 50% and macrofaunal abundance, biomass and richness by up to 76, 56 and 27% respectively. Our findings suggest that persistent inputs of hippo dung can act as an important stressor of benthic systems, leading ultimately to a loss of productivity. Accumulation of hippo dung over benthic habitats is therefore an important mechanism by which hippos indirectly structure aquatic ecosystems.