Continental Antarctica is a polar desert containing sparse pockets of vegetation within ice-free areas. Despite the recognized association between lichens, mosses and epiphytic diatoms, the environmental factors controlling diatom community structure are poorly understood. We investigated the association between diatom communities and host vegetation characteristics by experimentally adding nutrients and/or water to two bryophyte (healthy and moribund) and two lichen (crustose and Usnea) vegetation types in the Windmill Islands. Diatom communities were morphologically characterized, diversity indices calculated and differences between treatments, vegetation type and vegetation characteristics tested. We identified 49 diatom taxa, 8 of which occurred with > 1% relative abundance. Bryophyte and lichen vegetation harboured significantly different diatom communities, both in composition and diversity indices. Specifically, Luticola muticopsis was more prevalent in moribund bryophytes and crustose lichens, and Usnea lichens showed lower species richness than other types. While nutrient and water additions did not significantly alter diatom communities, diversity indices and some species showed relationships with vegetation physiological characteristics, notably %N and δ13C, suggesting the importance of ambient gradients in water and nutrient availability. Collectively, this work suggests that future conditions favouring the dominance of a particular vegetation type may have a homogenizing effect on the terrestrial diatom communities of East Antarctica.