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The food web structure within and adjacent to two permanently open estuaries with contrasting flow regimes along the south-eastern coast of South Africa was investigated employing stable isotope analysis. The Kariega Estuary is considered a freshwater-deprived system, while the Great Fish Estuary is freshwater-dominated due to an interbasin transfer scheme. Results from a study undertaken in April 2005 indicate that in the Kariega Estuary carbon sources assimilated by the zooplankton are derived from riparian vegetation in the upper reaches and from salt marsh and submerged macrophytes in the lower reaches of the system. In contrast, within the freshwater-dominated Great Fish Estuary the zooplankton appear to be sustained largely by allochthonous phytoplankton derived from freshwater inflow due to the interbasin transfer scheme. The magnitude of outflow of fresh water appears to play an important role as a carbon source for copepods and filter feeders in the marine environment adjacent to the Great Fish Estuary. The export of estuarine-derived particulate organic matter (POM) was evident up to 12 km downstream (west) of the Great Fish Estuary. Conversely, estuarine-derived POM appears to be utilised only directly adjacent to the Kariega Estuary mouth.

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The Kariega Estuary is a freshwater-deprived system due to numerous impoundments in the catchment. This system has had little or no horizontal salinity gradient over the last 15 years, with hypersaline conditions sometimes predominating in the upper reaches. Following high rainfall events in the catchment during the spring of 2006, including a flood event (approximate 1:10 year) in August 2006, a series of riverine pulses entered the estuary and a horizontal salinity gradient was established. This study examined the influence of this freshwater pulse on four components of the biota within the estuary, namely the zooplankton, and larval, littoral and demersal fishes. The study demonstrated that in three of these components elevated densities were recorded following the riverine input, with only the littoral fishes retaining an almost constant density. In addition, changes in the relative contributions of the estuarine utilisation classes for all three fish groups examined indicated that freshwater input into these systems positively influences the abundances. This has significant implications for water managers as it demonstrates the importance of an Ecological Reserve (defined as 'the water required to protect the aquatic ecosystems of the water resource') for this system.