Understanding the mechanisms underlying nutrient (nitrogen and phosphorus) and carbon cycling in reefs is critical for effective management. Research on reef nutrient and carbon cycling needs to account for (i) the contributions of multiple organisms, (ii) abiotic and biotic drivers, and (iii) a social-ecological perspective. In this paper, we review the mechanisms underlying nutrient and carbon cycling in reef social-ecological systems and analyse them using causal loop analysis. We identify direct and indirect pathways and feedback loops through nutrient and carbon cycles that shape the dominant benthic state of reefs: coral, algal, and sponge-dominated states. We find that two of three anthropogenic impact scenarios (size-selective fishing and land use change) have primarily negative consequences for coral and macroalgae via the nutrient and carbon cycles. A third scenario (runoff) has fewer negative impacts on sponges compared to other benthos. In all scenarios, frequent positive feedback loops (size-selective fishing: 7 of 12 loops; runoff: 6 of 9 loops; land use change: 8 of 11 loops) lead to system destabilization; however, the presence of multiple loops introduces avenues whereby reefs may retain coral dominance despite anthropogenic pressures. Context-specific information on the relative strength of loops will be necessary to predict future reef state.