Ongoing anthropogenic alterations of the biosphere have shifted emphasis in conservation biology from individual species to entire ecosystems. Modern measures of ecosystem change, however, lack the extended temporal scales necessary to forecast future change under increasingly stressful environmental conditions. Accordingly, the assessment and reconstruction of ecosystem dynamics during previous intervals of environmental stress and climate change in deep time has garnered increasing attention. The nature of the fossil record, though, raises questions about the difficulty of reconstructing paleocommunity and paleoecosystem-level dynamics. In this study, we assess the reliability of such reconstructions by simulating the fossilization of a highly threatened and disturbed modern ecosystem, a Caribbean coral reef. Using a high-resolution coral reef food web from Jamaica, we compare system structures of the modern and simulated fossil reefs, including guild richness and evenness, trophic level distribution, predator dietary breadth, food chain lengths, and modularity. Results indicate that despite the loss of species, guilds, and trophospecies interactions, particularly zooplankton and other soft-bodied organisms, the overall guild diversity, structure, and modularity of the reef ecosystem remained intact. These results have important implications for the integrity of fossil food web studies and coral reef conservation, demonstrating that fossil reef communities can be used to understand reef community dynamics during past regimes of environmental change.