Antarctic sea-floor communities are unique, and more closely resemble those of the Palaeozoic than equivalent contemporary habitats. However, comparatively little is known about the mechanisms and interactions that structure these communities or how they might respond to anthropogenic change. In order to investigate likely consequences of a decline or removal of key taxa on community dynamics we use Bayesian network inference to reconstruct ecological networks and infer changes of taxon removal. Here we show that sponges have the greatest influence on the dynamics of Antarctic benthic communities. When we removed sponges from the network, the abundances of all major taxa reduced by a mean of 42%, significantly more than changes of substrate. This study is the first time the cascade effects of removing key ecosystem structuring organisms has been inferred from statistical analyses of data from Antarctica. The South Orkney Islands, Antarctica, is an important ecosystem, as part of the locality is a Marine Protected Area. We demonstrate the importance of considering the community dynamics when planning ecosystem management.