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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.