Animal-mediated trophic resource transfers are important determinants of ecosystem functioning but are influenced by anthropogenic activities. In Africa, hippo defecation can influence aquatic processes at multiple scales, yet little is known about this phenomenon, with repercussions for estuarine benthic ecosystems being a particularly important knowledge gap. Here, we use in situ experiments to test responses of benthic meiofauna to dung loading in the St Lucia Estuary, which is Africa's largest estuarine ecosystem and home to one of South Africa's largest hippo populations. Findings indicate that high dung-loading levels negligibly affect meiofaunal community structure, with few community and individual metrics responding significantly. Richness and diversity displayed differential responses at the two experimental sites, with increasing trends occurring at the first site following dung addition but with a reversal at the second site. Similar findings were recorded for abundances of juvenile Assiminea cf. capensis (gastropod) and sizes of Nemata. In relation to prior findings for macrofauna from the same experiment, meiofaunal responses appeared weak and spatially idiosyncratic. We conclude that meiofauna are more robust and opportunistic than macrofauna in responding to dung-loading and suggest that high input rates may shift benthic communities from larger macrofaunal groups to smaller meiofaunal assemblages. We advocate that understanding traits of recipient assemblages that determine their susceptibility to hippo dung is necessary to develop a predictive understanding of this phenomenon. This would be especially important in protected areas that experience freshwater deprivation and support large and expanding hippo populations.