Carbon flow networks of the Kromme, Swartkops and Sundays estuaries, situated on the south coast of South Africa, were analysed using ecological network analysis. A major difference between the three estuaries is the freshwater inflow regimes: The Kromme Estuary receives very little freshwater (annual mean 0.07 m⁻³ s⁻¹), the Swartkops Estuary receives annually about 0.82 m⁻³ s⁻¹ while the Sundays Estuary receives on average about 2.74 m⁻³ s⁻¹ annually. Ecological network analysis revealed differences between most ecosystem attributes such as the cycling of carbon, trophic structure, the organisational and developmental status in terms of ascendency and redundancy, and regarding the contribution to and dependencies of compartments to and on one another in the network. Due to the lack of frequent freshwater inflow and consequently the renewal of the nutrient pool, the Kromme Estuary recycles most of its material and showed the highest detritivory/herbivory ratio (57:1), whereas the Sundays recycles the least proportion and had the lowest detritivory/herbivory ratio at 10:1. The Sundays Estuary, hitherto believed to be dominated by pelagic production, was found to rely more on the benthic biota in terms of carbon throughput as inferred from the contribution and dependency coefficients, than on pelagic communities. Due to the low rate of fresh water inflow into the Kromme Estuary, the absence of an axial salinity gradient, a comparatively high Finn Cycling Index of 40%, and the long water exchange time, this system appears to have developed into an “arm” of the sea. System level properties such as the A/C ratio, the Average Mutual Information index, and the food web connectance index, increase from the lowest values calculated for the Kromme Estuary, intermediate for the Swartkops Estuary, and highest for the Sundays Estuary, while the FCI followed an inverse trend between the three systems.