International treaties call for the protection of biodiversity in all its manifestations, including ecosystem and species diversities. The selection of most priority area networks focuses, however, primarily on species richness and occurrence. The effectiveness of this approach in capturing higher order manifestations of biodiversity, that is ecosystem and environmental diversity patterns, remains poorly understood. Using a case study of birds and environmental data from South Africa and Lesotho, we test how complementary networks that maximise species diversity perform with regard to their representation of ecosystem and environmental diversity, and vice versa. We compare these results to the performance of the existing reserve network. We conclude that focusing on any single biodiversity component alone is insufficient to protect other components. We offer explanations for this in terms of the autocorrelation of species diversity in environmental space.