Report No: 756/1/03

February 2003


The work described in this report is part of more comprehensive investigations undertaken by the Consortium for Estuarine Research and Management (CERM) for the Water Research Commission (WRC) to improve the predictive capabilities on the effects of changes in river flow on the physical and ecological conditions in estuaries. Focus of this particular research programme was aimed at increasing our knowledge of the river-estuary interface (REI) region of selected Eastern Cape estuaries, and the Gamtoos system in particular. The REI region is defined as that part of an estuary where river and estuarine waters mix, and where the vertically integrated salinity is usually less than 10‰.

The following global hypothesis, developed by the research team conducting this project, was used to guide the different studies:

"The structure and functioning of the river-estuary interface region is governed primarily by the quality, quantity and supply pattern of fresh water received. Furthermore, the interface region has strong influences on the physico-chemical as well as the biological structure and functioning of the entire system."

Estuarine hydrodynamics

Predictions of changes in the physical conditions in the Gamtoos Estuary under different river flow conditions and especially of the effects on salinity distributions in the estuary using the Mike-11 modelling system were undertaken. Several important results were obtained from the model, which played a major role in the complementary investigations on the ecological components of the study.

A large number of model simulations were undertaken to determine the salinity distributions in the Gamtoos Estuary for different river flows. The results are included in the report as graphs for high and low neap and spring tides. These simulations were also undertaken for pre-1996 flood and for post-1996 flood conditions, with significant differences in salinity distributions being found as a result of the scouring effect of these floods. The model results were also used to determine the volumes of water in the estuary below (and between) selected salinity levels of 5, 10, 15,20, 25, 30 and 35‰ for different river flows under pre- and post flood conditions. In this manner the volume of available habitat (based on salinity) for aquatic organisms could be calculated.

Water column and porewater nutrients

Variations in the nutrient status of the Gamtoos Estuary could not be directly linked to riverine flow. Freshwater inputs under base flow conditions (0.35 to 1.6 m3 s-1) did not influence mean estuarine nutrient concentrations significantly. However, phosphate concentrations were positively correlated with freshwater input (r = 0.67; P < 0.05). Investigations of nutrient concentrations between spring and neap tides showed that tidal movement also had no significant influence on nutrient status. As freshwater inflow had no direct, significant influence on water column nutrient status, the amount of freshwater inflow required for consistent nutrient inputs to the estuary is unknown. However, it is predicted that a reduction in base flow will influence water column nutrient status through its influence on estuary mouth phase. Closed vs open mouth phases are likely to have different effects on the storage, release and exchange of nutrients within the estuary and between the estuary and sea.

Although some nutrient species were found to occur at higher concentrations in the upper reaches (vertically averaged salinity of 17‰ and below) of the Gamtoos Estuary, it was not possible to identify a REI confined within a certain salinity range for any of the nutrients measured. Overall, concentrations decreased towards the mouth in the case of nitrate, nitrite, dissolved organic carbon (DOC) and nitrogen (DON), particulate organic nitrogen (PON) and total particulate phosphorus (TPP). Plots of nutrients against salinity did not reveal strong conservative behaviour for most nutrients, which points towards biological transformation and/or non-point source additions of nutrients along the estuarine gradient.

Although freshwater inputs did not significantly influence the inorganic nutrient status of Gamtoos interstitial waters, sediment porewater quality did significantly affect benthic water nutrient status. Porewater concentrations of nitrate and nitrite were 5 to 10 times higher than respective water column concentrations, while no concentration gradients existed between the water column and porewaters for ammonium and phosphate. Nitrate, nitrite, and ammonium porewater concentrations were significantly correlated with respective concentrations in the bottom waters of the water column (r = 0.58, P < 0.001; r = 0.24, P < 0.05; r = -0.26, P < 0.05, respectively). Both porewater and bottom water phosphate concentrations were very low in the Gamtoos Estuary, indicating a phosphate- limiting environment in this system.

Estuarine microalgae

A primary objective of this particular study was to assess the effects of Gamtoos River flow on the community structure and biomass of estuarine microalgae. The investigation showed that as flow increased the average nitrate in the estuary increased. A base flow of approximately 1.0 m3 s-1 resulted in the highest microalgal biomass as indicated by phytoplankton and benthic microalgal chlorophyll-a concentrations. At most flows, the sites where phytoplankton chlorophyll-a (g 1-1 ) was highest was near (1.5 km) to the position where the vertically averaged salinity was 10‰ (i.e. mostly 12.5 to 14.5 km from the mouth). Subtidal and intertidal benthic chlorophyll-a values were highest at flows of 1.0 (57.7 kg 0.4 SE) and 1.2 m3 s-1 (8.7 kg 0.1 SE) respectively. Benthic microalgal biomass was highest in regions where the salinity was 10 to 15‰, and was positively correlated with porewater phosphate concentrations.

Results from this study provide a preliminary tool that can be used to estimate the base flow I for maximum phytoplankton biomass from known estuary volumes. If the total volume of the estuary is 3.6 x 106 m3 the estuary will be completely flushed in about 42 days at a flow rate of 1.0 m3 s-1. To obtain maximum microalgal biomass a residence time of 3 spring tidal cycles (42 days) is required.

From this, if the estuary volume is known, then the base flow required can be determined from the formula;

Base flow (m3 s-1) = (8.7 x Volume of estuary)/31536000
where; 8.7 = number of times an estuary is flushed per year at a residence time of 42 days
Volume of estuary = volume in m3
31536000 = number of seconds in a year

The succession of phytoplankton groups as a result of base flow changes was also investigated. Phytoplankton were identified into five groups (diatoms, flagellates, dinoflagellates, chlorophytes and cyanophytes), counted and analysed in relation to flow rate. In both the Kromme and Gamtoos estuaries, flagellates increased as flow decreased while diatom numbers peaked at a flow of approximately 1.0 m3 s-1. These two were the dominant groups of phytoplankton at most flows in the Gamtoos and at all flows in the Kromme Estuary. Chlorophytes, dinoflagellates and cyanophytes increased as flow decreased and were most abundant in the shallow upper reaches of the Gamtoos Estuary. Multivariate analyses were used to identify phytoplankton community structure in relation to flow. No differences in phytoplankton community structure were found inside the REI compared to outside of the REI.

Estuarine invertebrates

Studies on both the benthic invertebrates and zooplankton showed that patterns of species distribution between the mouth and upper Gamtoos estuary indicate clear zonation of animal assemblages. Pelagic and benthic assemblages in the REI region differ significantly in their species assemblages and abundance of component species compared to species composition farther downstream. Ecological communities of low salinity regions are therefore distinct in their biological structure.

Benthic communities of the REI are not only unique in their biological structure but display a different trophic organisation compared to assemblages in more saline waters. Filter-feeders dominate low salinity regions, possibly as a response to the high phytoplankton production in this sector, while surface-active deposit feeders dominate downstream in the lower estuary. In addition, food web components in the REI carry distinct carbon 'signatures' compared with organisms in other regions of the estuary. Carbon isotope ratios of primary producer's (phytoplankton, benthic microalgae, macrophytes) increase significantly and linearly with salinity. Similarly, gradients in carbon isotope composition are mirrored by equivalent relationships between delta 13C and salinity in consumers (prawns, amphiods, crabs, bivalves). This systematic shift in carbon composition across the salinity spectrum in both producers and consumers suggests that production and consumption of organic matter are spatially restricted to particular reaches of the estuary. Processing of energy through the food web within a salinity zone (e.g. in the REI) may therefore lead to limited transport and mixing of organic matter between salinity zones.

Carbon in selected top fish predators is ultimately derived from benthic microalgal production. The transfer of microalgal carbon to these higher trophic levels is channelled via two steps, a grazing of benthic microalgae by mugilid species, and a consumption of these taxa by piscivorous predators. These results stress the energetic importance of benthic microalgae in supporting fish production in the estuarine environment. In addition to benthic microalgae, which form the base of a clear trophic transfer route to piscivorous fish, a second energy pathway that originates from phytoplankton is important for higher trophic levels. Benthic invertebrates that assimilate mostly phytoplankton make a substantial contribution to the diet of benthivorous fish that are abundant in the REI region. Similarly, zooplankton grazing on phytoplankton is the intermediate trophic step that links pelagic primary production with pelagic zooplanktivorous fish. Since freshwater inflow promotes productivity of both benthic and pelagic microalgae in estuaries, supply rates of freshwater to estuaries are clearly a dominant structuring force for estuarine communities at several trophic levels.

Estuarine fishes

A primary objective of this study was to examine the fish assemblages in the REI region of the Great Fish and Kariega estuaries, and relate these structures to riverine influences in particular. Since the Kariega Estuary did not possess a significant REI region due to a lack of riverine flow, the geographical headwaters became a focus of research attention in this particular system.

The fish assemblages along the length of the Kariega and Great Fish estuaries exhibited a clear zonal trend, with the REI/headwater region forming a distinct but different grouping in both systems. Multivariate analyses, which examined the possible influence of various abiotic variables in structuring the fish assemblages associated with the different reaches in the two estuaries, indicated that a combination of variables produced the best correlations. Salinity has traditionally been regarded as one of the more important structuring forces in estuaries and was found to be an important factor in the Great Fish but not in the Kariega system.

In the Great Fish Estuary there were distinct trends between river flow rate and the species assemblages found within the different reaches of the system. Fish abundance in the REI region decreased with increasing riverine flow, with the highest abundance of fish being recorded under flow conditions <10 x 106 m3 month-1. Species composition also changed, with the marine species contribution to the REI fish assemblage dropping from 60% under lower flow conditions to <30% during periods of elevated riverine flow (>20 x 106 m3 month-1). A major increase in river flow results in an overall decline in fish abundance throughout the system, with flooding having the potential to cause extensive mortalities within the estuary.

The quality of freshwater entering an estuary may also affect the fish assemblages in the REI region. The high conductivity levels of the water in the Great Fish River may reduce the osmotic I stress experienced by marine species in brackish water and therefore assist the penetration of these species into the upper reaches of the estuary and river. Conversely, floods reduce the high conductivity levels of river water and result in a decrease in marine species in the REI region and adjoining river.

Conservation and management

Important issues/principles addressed by this research programme, which will influence the conservation and management of Eastern Cape estuaries, and the REI region in particular, are outlined below.

Estuarine hydrodynamics

Water column and porewater nutrients

Estuarine microalgae

Estuarine invertebrates

Estuarine fishes


Prior to the initiation of this multi-disciplinary and multi-institutional research programme, the influence of river flow rates on biotic and abiotic components in the river-estuary interface zone was poorly understood. Permanently open Eastern Cape estuaries were the focus of this study because the catchments of these systems are a primary freshwater source when it comes to supplying both urban and rural users. A Water Research Commission sponsored research programme has since been initiated to examine the REI region of temporarily open/closed estuaries along the South African coast.

For the purposes of the Eastern Cape REI study, the following primary conclusions emerged:

  1. Elevated river flow rates into the Gamtoos Estuary increased the size of the REI zone both longitudinally and in terms of volume. A flow rate of between 0.8 and 1.2 m3 s-1 produced a maximum phytoplankton biomass in the estuary but there was no clear relationship between measurable nutrient content in the water column and phytoplankton biomass.
  2. River flow rate and the size of the REI were shown to have a major effect on the distribution and community structure of aquatic invertebrates. Benthic invertebrates of the Gamtoos REI region had a different species composition and abundance to those found in the more saline estuarine reaches. Similarly, estuary-associated fishes in the Great Fish Estuary showed a distinct longitudinal zonation pattern that was related to salinity changes, with the REI region playing an especially important nursery role for certain angling fish species.
  3. From the above we can conclude that the maintenance and productivity of the REI zone depends on an adequate supply of river water (measured in terms of both quantity and quality) entering the estuary. In future the management and implementation of the Water Reserve, as required by the National Water Act (No. 36) of 1998, should address not only the requirements of the lower and middle estuarine reaches but also the very important REI region which, in turn, affects the entire system.