The effect of replacement of live coral cover by epilithic algae on patterns and magnitudes of carbon flux is examined for the shallow front slope of a midshelf reef in the Great Barrier Reef (GBR). The shift in structure to an algae-dominated system realises lower rates of benthic primary production, and thus system size and activity are reduced. With loss of coral cover, the proportion of the total flow that is recycled and transferred to the detritus pool increases (although the structure of recycling is not affected), and the balance of pathways in the network is changed. In the coral-dominated state, carbon fixed by zooxanthellae is used indirectly by most organisms in the system. Differences between the coral- and algae-dominated systems were much greater than differences between two scenarios for the algae-dominated state whereby grazer-response is included or excluded. -from Authors