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) complex of Australia. A steady-state network of carbon exchange among 19 trophic compartments is constructed for the coral-dominated state. From this, 2 scenarios for patterns of carbon flux when algae dominate are derived, viz.(1) the increase in algal production is channeled to detrital pathways (grazers do not respond), and (2) grazers utilise the increase in production of algal carbon so that transfers to detritus and grazers are in the same proportion as occurs when coral cover is high. The 3 models summarise current knowledge of carbon flux on GBR reef fronts and are compared using network analysis. Because fluxes in the reef front zone are dominated by exogenous imports and exports as a result of the high volume of water passing around and over the reef, the analyses ignore advective fluxes across the zone that are not internalised.The shift in structure to an algae-dominated system realises lower rates of benthic primary production, and thus system slze and activity (i.e. total system throughput, internal throughput, development capacity and ascendancy) are reduced, suggesting a disturbed system. 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: average path length increases, while the average trophic level of most of the second order consumers, and trophic efiiciencies of most trophic categories, decreases. Also, there are marked changes in dependencies of particular trophic groups on others. The analysis shows that, in the coral-dominated state, carbon fixed by zooxanthellae is used indirectly by most organisms in the system, even those seemingly remotely connected. Differences between the coral-and algae-dominated systems were much greater than differences between the 2 scenarios for the algae-dominated state. However, the exact fate of additional algae-derived carbon In the system is an important consideration since the 2 scenarios for the algae-dominated state yielded dissimilar values for some parameters (e.g. flow diversity, trophic dependencies and effective trophic levels of some compartments, relative importance of recycling, trophic efficiency of some trophic categories).