Thesis (MSc (Geography and Environmental Studies))--University of Stellenbosch, 2007. / In South Africa, as a result of limited resources and capacity, the governance and management of estuaries occur on an ad hoc basis, with decisions about an estuary’s freshwater-flow requirements, water quality, living-resources management, mouth management and protection status being made on a largely uncoordinated and non-strategic basis. This study is aimed at developing an understanding of the opportunities and constraints affecting estuarine management at a regional scale. The objectives of this study were to: 􀂃 Review relevant policy and legislation governing estuarine management in South Africa; 􀂃 Discuss the current status of regional estuarine management in South Africa; 􀂃 Review international literature for potentially applicable management guidelines; 􀂃 Construct a management protocol for estuarine management in South Africa; 􀂃 Apply this protocol in a South African setting; and 􀂃 Recommend improved measures for regional estuarine management. The main outcome of the study was the development of the proposed National Estuarine Management Protocol, which is currently in the process of being incorporated into the National Environmental Management: Coastal Zone Bill. The CAPE Estuaries Programme was developed to test the proposed Protocol in a regional setting. The study concluded that there was an urgent need for a more holistic regional approach to estuarine management but that the proposed framework and protocol would be successful only if, in addition, they were supported by an understanding of the biophysical estuarine processes and management constraints operating at the local level.

Temporarily open/closed estuaries (TOCE’s) are the numerically dominant type of estuary accounting for ≈ 70 % of all estuaries along the South African coastline. Despite their numerical dominance, aspects of the biology of organisms within these systems, particularly macrocrustacea remain poorly understood. This study firstly assessed the abundance and biomass of the most common isopod, Exosphaeroma hylocoetes, in three Eastern Cape TOCE’s, (the West Kleinemonde, East Kleinemonde and Kasouga Estuaries), and their response to mouth breaching events. This study was followed by aspects of the biology of the isopod including their utilisation of submerged macrophytes as a refuge from predation and/or possible food source, as well as the growth rates of the isopods in the laboratory under different environmental conditions. Mean isopod abundances and biomasses ranged between 0 and 4 791 ind. m⁻² and 0 and 9.65 mg dwt. m⁻² in the West Kleinemonde Estuary and between 0 and 108 ind. m⁻² and 0 and 0.318 mg dwt. m⁻² in the nearby East Kleinemonde Estuary. In the Kasouga Estuary, the values ranged between 0 and 3 650 ind. m⁻² and 0 and 5.105 mg dwt. m⁻². Temporal and spatial changes in the abundance and biomass of E. hylocoetes within the three systems was primarily linked to mouth phase, with populations declining when the mouth was open and to a lesser extent, seasonality. In all three estuaries maximum isopod abundances and biomasses were recorded in their middle and upper reaches, which could be ascribed to the presence of submerged macrophytes particularly Ruppia maritima, in two of the estuaries. Males (5.71 ± 0.41 mm) were significantly larger than females (3.99 ± 0.26 mm), but the sex ratios were skewed in favour of females, (a common feature in many isopod populations). Females were found carrying brood throughout the study, releasing offspring directly into the water column, to allow recruitment to the populations. The larger the female, the larger the brood carried (up to a maximum of 72 embryo/mancas). Results of laboratory experiments indicate that the close association of Exosphaeroma hylocoetes with submerged macrophytes is a result of the plant stands providing a refuge against predation by selected ichthyofauna. However stable carbon isotope and fatty acid analyses indicate that E. hylocoetes made use of ephiphytic algae and detritus on the stems of R. maritima, rather than the submerged macrophyte itself. There were no significant differences in the growth rates of male and female isopods at combinations of temperature (15 and 25 °C) and salinity (15 and 35 ‰). Laboratory growth studies revealed that males lived longer than females (25.77 ± 3.40 weeks vs 21.52 ± 3.00 weeks), and therefore achieved larger overall size. Females, however, reached sexual maturity (at 2.5 mm) at a faster rate (two to four weeks) than males (5.5 mm after 6.5 to 11 weeks), dependent on temperature. Exosphaeroma hylocoetes with its association with submerged macrophytes, early maturity, its growth rates and longevity, female-biased sex ratios and year-round breeding, all contribute to its success in temporary open/closed estuaries.

The coastal transition zone (CTZ), which links the terrestrial and marine environments, has been identified as a region of high biological diversity and elevated production. Results of studies conducted in the northern hemisphere indicate that the links between estuaries and the adjacent marine environment is critical to ecological functioning within the CTZ. This study assessed the influence of selected estuaries with different hydrodynamic characteristics on the adjacent marine environment along the south-eastern coastline of southern Africa. Four estuaries were examined, including two permanently open systems, the fresh water deprived Kariega and fresh water dominated Great Fish, and two temporarily open/closed estuaries (TOCE), the Kasouga and East Kleinemonde. Results of the study indicated that outflow of estuarine water from the Great Fish Estuary contributed to a plume of less saline water being evident within the adjacent marine environment. The plume of water was associated with increased zooplankton biomass and particulate organic matter (POM) and chlorophyll-a concentrations. Adjacent to the Kariega Estuary, no evidence of fresh water outflow into the marine environment was observed. However, in the sea directly opposite the mouth of the estuary an increase in zooplankton abundance and biomass was evident. Results of numerical analyses indicated that the increase in zooplankton abundance observed adjacent to the mouth of both permanently open estuaries could not be attributed to the export of zooplankton from the estuary, but rather the accumulation of marine species within the region. The mechanisms responsible for this accumulation were not determined, but it was thought to be associated with increased food availability in the estuarine frontal zone. A similar, but less dramatic biological response was also observed in the marine environment adjacent to the two TOCEs. It is suggested that the increase in biological activity within these regions could be ascribed to seepage of estuarine or ground water through the sand bar that separates these estuaries from the sea. Results of stable carbon isotope analyses indicated that both the Great Fish and Kariega estuaries exported carbon to the nearshore marine environment. The area influenced by estuarine derived carbon was dependent on the volume of estuarine outflow to the marine environment. Adjacent to the fresh water dominated Great Fish Estuary, estuarine derived carbon was recorded up to 12km from the mouth, while adjacent to the fresh water deprived Kariega, estuarine derived carbon was only evident directly opposite the mouth. The recruitment of macrozooplankton (> 2cm) into the fresh water deprived Kariega Estuary was in the range recorded for other permanently open southern African estuaries with higher fresh water flow rates. This indicates that the mechanisms which allow estuarine dependent larvae to locate and enter estuaries are not related to fresh water inflow. In conclusion, this study has demonstrated that despite their small size relative to European and North American systems, South African permanently open and temporarily open/closed estuaries also influence biological activity within the adjacent nearshore marine environment.

An estuary, according to the National Water Act of 1998, is a partially or fully enclosed body of water which is open periodically or permanently to the sea within which the sea water can be diluted, to an extent that is measurable with freshwater from inland. Estuaries and the lands surrounding them are places of transition from land to sea, and from freshwater to saltwater. Although influenced by the tides, estuaries are protected from the full force of ocean waves, winds, and storms by the reefs, barrier islands, or fingers of land, mud, or sand that surround them. South Africa’s estuaries are important and irreplaceable habitats, especially for prawns, fish, wading birds and mangroves. They are home to numerous plants and animals that live in water that is partly fresh and partly salty. Estuaries are also homes to growing coastal communities as increasing number of people occupy watersheds. However, estuaries are also threatened. One of the threats is reduced river water inflow. This study applies the contingent valuation method (CVM) to elicit user’s willingness to pay to mitigate the negative impacts of reduced freshwater inflow into selected five Eastern Cape and Kwazulu-Natal estuaries: the Sundays, Gamtoos, Mdloti, Mgeni and Mvoti estuaries. In addition to the contingent valuation method, the travel cost method was used to generate comparative values. The contingent valuation method is a technique to establish the value of a good (or service) that is not bought or sold in an actual market. The CVM establishes the economic value of the good by asking the users of an environmental good to state their willingness to pay (WTP) for a hypothetical project to prevent, or bring about, a change in the current condition of the environmental good. The users’ WTP is aggregated to establish a total willingness to pay (TWTP) for the population of the users of the environmental good.

Larval fish and zooplankton assemblages were studied in nine south and west coast estuaries in the cool-temperate and the cool/warm-temperate boundary region between June 2003 and March 2004. This study served to provide new information on previously unstudied estuaries and expand on existing knowledge of larval fish and zooplankton assemblages associated with various estuary types. The south and west coast estuaries sampled in this study showed lower salinities (12.2 - 13.7), lower water temperatures (14.5 - 16.9 °C) and higher turbidities (k = 0.02 - 0.04) in winter and spring while higher salinities (21.7 - 21.8), higher water temperatures (21.7 - 23.1°C) and lower turbidities (k <0.02) were observed in summer and autumn. Mean winter and summer water temperatures in estuaries were lower than those observed in warm-temperate and subtropical systems by other researchers. A total of 49274 larval fishes were caught, comprising 9 orders, 20 families, 29 genera and 47 taxa. The clupeid Gilchristella aestuaria (78.8 %) dominated the larval fish assemblages and occurred in all estuaries. The majority (70 %) of identified species are endemic to southern Africa and 96.4 % of larval fishes caught were estuary-resident species. The zooplankton study yielded a total of 44 taxa, comprising 7 phyla, >20 orders and >35 families. The copepod Pseudodiaptomus hessei dominated (59 %) the zooplankton and occurred in similar densities to those observed in other South African estuaries. Larval fish and zooplankton varied across seasons, peaking simultaneously in summer although zooplankton showed additional density peaks during the closed phase of some estuaries. Both plankton components were more abundant in the oligohaline and mesohaline zones within the estuaries. Freshwater input, estuary type and the biogeography of the area influenced the composition and structure of larval fish and zooplankton assemblages in these estuaries. The findings suggest that the estuaries are functioning as successful breeding areas for the larvae of endemic estuary-resident fish species and that these estuaries have to be managed to ensure an adequate freshwater supply to maintain the biological integrity of the ecosystem, specially the maintenance of the highly productive River-Estuary Interface (REI) regions.

The ichthyofaunal community structure, population dynamics and movement patterns in the small temporarily open/closed (TOCE) Grant’s Valley estuary, situated along the Eastern Cape coastline, were investigated over the period May 2004 to April 2005. Community structure in the littoral zone was assessed, while growth of selected ichthyofaunal species was investigated using the MULTIFAN model. Population size was assessed using mark recapture models and movement within the estuary using the Hilborn (1990) model. Total ichthyofaunal densities and biomass within the littoral zone ranged between 0.31 to 21.45 fish m⁻² and 0.20 to 4.67 g wwt m⁻², with the highest values typically recorded during the summer. Results of the study indicated that the ichthyofaunal community structure within the estuary was closely linked to the mouth phase and the establishment of a link to the marine environment via overtopping events. In the absence of any link to the sea, the ichthyofaunal community was numerically dominated by estuarine resident species, mainly Gilchristella aestuaria and to a lesser extent, by the river goby, Glossogobius callidus which collectively comprised ca. 88% of all fish sampled. The establishment of the link to the marine environment contributed to an increased contribution of marine breeding species (e.g. Rhabdosargus holubi, Myxus capensis and Atherina breviceps) to the total ichthyofaunal abundances. In contrast, total ichthyofaunal biomass was almost always dominated by marine breeding species by virtue of their larger sizes. Results of hierarchical cluster analyses did not identify any spatial patterns in the ichthyofaunal community within the littoral zone. Results of MULTIFAN analysis indicated estuarine resident fish species bred over an extended period with peaks occurring in the summer months. Conversely, marine breeding fish were shown to recruit into the estuary following overtopping and breaching events. Results of the mark-recapture experiment indicated a population of ca. 12 000 (11 219 – 13 311) individuals greater than 50mm SL. Marine-breeding species (R. holubi, Monodactylus falciformis, and two mullet species) numerically dominated the ichthyofauna, possibly as a result of their effective use of overtopping events. The two mullet species, M. capensis and Liza richardsonii, and the Cape stumpnose, R. holubi moved extensively throughout the estuary, while the remaining species exhibited restricted movement patterns possibly due to the preference for refuge and foraging areas associated with reed beds. The observed movement patterns of individual fish species appeared to be associated with both foraging behaviour and habitat selection.

The main aim of this study was to assess the “top-down” and “bottom-up” control of bacterial production in the small temporarily open/closed East Kleinemonde Estuary, situated on the south-eastern coastline of southern Africa. Spatial and temporal patterns in bacterial abundance, biomass and production and the importance of abiotic and biotic factors were investigated over the period May 2006 to April 2007. The trophic interactions between bacteria, phytoplankton, nanoflagellates (< 20 μm), microzooplankton (< 200 μm) and mesozooplankton (< 2 000 μm) were investigated during winter and summer. Bacterial abundance, biomass and production ranged between 1.00 × 10⁹ and 4.93 × 10⁹ cells 1⁻¹, 32.4 and 109 μg C 1⁻¹ and 0.01 and 1.99 μg C 1⁻¹ h⁻¹, respectively. With a few exceptions there were no spatial patterns in the values. Bacterial abundance, biomass and production, however, demonstrated a distinct temporal pattern with the lowest values consistently recorded during the winter months. Nanoflagellate and bacterial abundances were significantly correlated to one another (lower reaches: r = 0.818, p < 0.001; middle reaches: r = 0.628, p < 0.001; upper reaches: r = 0.484, p < 0.05) suggesting a strong predator-prey relationship. The frequency of visibly infected bacterial cells and the mean number of virus particles within each bacterial cell during this study demonstrated no temporal or spatial patterns and ranged from 0.5 to 6.1 % and 12.0 to 37.5 virus particles per bacterium, respectively. Viral infection and lysis was thus a constant source of bacterial mortality throughout the year. The estimated percentage of bacterial production removed by viral lysis ranged between 7.8 and 88.9% of the total which suggests that viral lysis represented a very important source of bacterial mortality during this study. The biological interactions between the selected components of the plankton community demonstrated that among the heterotrophic components of the plankton, the nanoflagellates were identified as the most important consumers of bacteria and small phytoplankton cells (< 20 μm). In the presence of microzooplankton the impact of the nanoflagellates on both the bacteria and phytoplankton was reduced, indicating that larger heterotrophs were preying upon the nanoflagellates. Mesozooplankton, however, appeared to exert the greatest impact on nanoflagellates. In the cascading experiments, the data suggest that mesozooplankton consume nanoflagellates, which resulted in a decrease in the predation impact of these organisms on the bacteria. This result is consistent with predator-prey cascades. The presence of the larger heterotrophs therefore, mediates the interactions between the primary bacterivores, the nanoflagellates, and the bacteria within the temporarily open/closed East Kleinemonde Estuary.

The spatial and temporal patterns in the ichthyofaunal community composition and structure in Taylor’s salt marsh and adjacent eelgrass beds (Zostera capensis) in the Kariega Estuary, was investigated every two months between May 2006 and March 2007. Total ichthyofaunal abundances and biomass in the salt marsh ranged between 0.55 and 21.7 ind.10m-2 and between 0.03 and 1.9 g.wwt.10m⁻², respectively. There were no significant spatial patterns in the values evident (P > 0.05 in all cases) although seasonal trends were marked, with highest values consistently recorded during the warmer summer months. Investigations into the community structure showed that the ichthyofaunal community within salt marsh was composed almost exclusively of juveniles of estuarine dependant (category II) species, mainly juvenile Mugilidae (<20mm SL) that comprised up to 83% of all fish sampled. Hierarchical cluster analysis and multidimensional scaling did not identify any distinct spatial patterns in the ichthyofaunal community within the salt marsh. The absence of any spatial patterns in the community structure could be related to the absence of any significant spatial patterns in the physico-chemical (temperature, salinity and dissolved oxygen concentrations) and biological (water column and microphytobenthic algal concentrations) variables within the salt marsh (P > 0.05 in all cases). Temporal shifts in the ichthyofaunal community structure within the salt marsh were, however, evident largely reflecting the breeding cycles of individual species within the sub-region. Within the adjacent eelgrass beds, total ichthyofaunal abundances and biomass ranged between 8.4 and 49.4 ind.10m⁻² and between 2.9 and 94.5 g.wwt.10m⁻², respectively. Once again there were no distinct spatial patterns in the abundance and biomass values evident although seasonal patterns were marked. In contrast to the salt marsh, within the in the eelgrass community, there were a large number of adult individuals recorded. Again category II species, the estuarine dependent species, were numerically and gravimetrically dominant. The dominance of category II species reflects the marine dominance of Kariega Estuary. The remaining estuarine utilisation categories did not contribute significantly to abundance or standing stock totals. Hierarchical cluster analysis showed that the salt marsh and eelgrass beds represented two distinct habitats within the Kariega Estuary. Within the salt marsh, the family Mugilidae were numerically dominant contributing 83% of the total catch. Within the eelgrass beds, the sparid, Rhabdosargus holubi and representatives of the family Gobidae contributed 36.3% and 33.9% respectively to the total catch. Estuaries with a wide range of microhabitats have been demonstrated to support a more diverse ichthyofaunal community. Shallow water habitats in general are important areas for juvenile fish within estuaries. Taylor’s salt marsh provides an alternative shallow water habitat, occupied by a distinct ichthyofaunal community composition, with increased food availability and decreased predation pressure, for a wide range of fish species.

The larval fish and zooplankton assemblages were studied in the permanently open Sundays Estuary on the south-east coast of South Africa, using standard boat-based plankton towing methods. A total of 8174 larval and early juvenile fishes were caught, representing 12 families and 23 taxa. The Clupeidae, Gobiidae and Blenniidae were the dominant fish families. Common species included Gilchristella aestuaria, Caffrogobius gilchristi, Omobranchus woodi, Liza dumerilii, Glossogobius callidus and Myxus capensis. Estuarine resident species (Category I) predominantly in the preflexion developmental stage, dominated the system. A total of 19 zooplankton taxa were recorded. Copepoda dominated the zooplankton community. Dominant species included Pseudodiaptomus hessei, Acartia longipatella, Halicyclops sp., Mesopodopsis wooldridgei, and the larvae of Paratylodiplax edwardsii and Hymenosoma orbiculare. Mean larval fish density showed similar trends seasonally, spatially and across salinity zones, with mean zooplankton density in the Sundays Estuary. Gut content analysis of five larval fish species: Gilchristella aestuaria, Pomadasys commersonnii, Monodactylus falciformis, Myxus capensis and Rhabdosargus holubi, revealed species specific diet and prey selection. Although larval fish diet contained a variety of prey items, guts were dominated by P. hessei, chironomid larvae, Corophium triaenonyx, copepod eggs and insect larvae. Physico-chemical drivers and the interactions between these two plankton communities provide information that enables a more holistic view of the dynamics occurring in the Sundays Estuary planktonic ecosystem.

This study investigated the response of the macrophytes in St Lucia Estuary, northern KwaZulu-Natal to drought. The present distribution of vegetation (2010 / 2011) was mapped and changes over time recorded from past aerial photographs. The changes in macrophyte cover in response to environmental factors (sediment and groundwater characteristics) was measured along four transects in 2010 and compared with results from previous years, in 2005 and 2006. In the current study, 1960 images were digitized to illustrate macrophyte distribution and cover of the Narrows, Makakatana and the Eastern Shores during a low rainfall period which started in 1958. The 2001 images were digitized to illustrate vegetation distribution and cover of the same area prior to the current drought which started in June/ July 2002. The 2008 images were digitized to illustrate vegetation distribution and cover of estuarine vegetation within the floodplain during the drought (after 6 years). The sites were visited in June 2011 for verification of the distribution and boundaries of each macrophyte habitat. The area covered by the water column varied over time. In 1960 during a low rainfall period the water was 32705 ha, 33320 ha in 2001 and reduced to 30443 ha in 2008. The area cover of inundated and dry reeds fluctuated with the water level. Under high water levels, low-lying areas such as Fanies Island and Selley‟s Lake were flooded and under low water levels, intertidal sand and mudflats were exposed and colonised by succulent salt marsh (Sarcocornia spp. and Salicornia meyeriana). Similar conditions were observed at Makakatana. Mangroves were observed from the mouth to the Forks. Avicennia marina was the dominant mangrove species and primary colonizer of dredge spoil. The area cover of mangroves in the vicinity of the mouth fluctuated as a result of fluctuating water levels, dredging operations, excavation of the Back Channel and Cyclone Gamede which killed intertidal vegetation. Between 2001 and 2008, mangrove expansion was faster in the Mfolozi Swamps area (± 1.4 ha yr -1) compared to the Narrows (± 0.4 ha yr -1). Long term monitoring transects were set up in 2005, at Makakatana, Charters Creek, Catalina Bay and at Listers Point to document changes in sediment conditions and vegetation cover. These were sampled in July 2005, October 2005, February 2006 and May 2010. Silt was the dominant particle size at Catalina Bay, Charters Creek and Makakatana. At Makakatana, average ground water salinity was 17.2 ± 6.6 ppt, 4.1± 4.9 ppt at Catalina Bay and 32.9 ± 19.3 ppt at Charters Creek. Drought resulted in the accumulation of salt on the surface sediment layer at Listers Point and Charters Creek due to low rainfall. Listers Point, the site with the lowest freshwater input and habitat diversity had the lowest macrophyte species richness with only three species. The dominant species at this site were Sporobolus virginicus and Chenopodium album L. which are highly salt tolerant species. Catalina Bay had the highest species richness (18 to 27); as a result of freshwater input via groundwater seepage from the sand dune aquifers on the Eastern Shores. Along the Eastern Shores, vegetation was dominated by species of Cyperaceae, Juncaceae and Juncaginaceae. Fluctuations in groundwater depth were observed at all sites, Listers Point groundwater depth in February 2006 was 80 cm and the ground water level was not reached during the May 2010 field trip. During the May 2010 field trip, the water column salinity of the St Lucia system was highly variable, Makakatana had the lowest water column salinity of 7.1 ppt, 42.1 ppt at Catalina Bay, 44 ppt at Charters Creek and Listers Point had the highest water column salinity of 95 ppt. An assessment of the changes in macrophyte cover along the transects showed that cover fluctuated in response to rainfall, water level and drought. At Listers Point, there was a continuous decline in the abundance of Sporobolus virginicus over time which was sparsely distributed in the first 40 m of the transect. Sarcocornia natalensis, a succulent and obligate halophyte, was recorded, in areas with high sediment conductivity. In May 2010, bare ground increased to an average percentage cover of 96.5% and was covered with dead organic matter and a salt crust at Listers Point. At Makakatana, there was a significant decrease in bare ground from July 2005 to May 2010 (H = 24.58, N = 197, p<0.001) as bare areas were colonized by salt marsh. Multivariate analysis showed that the abundance of Sporobolus virginicus was positively influenced by sediment moisture content and Paspalum vaginatum abundance was strongly influenced by the water column salinity. At Catalina Bay, low sediment conductivity at the groundwater seepage area resulted in terrestrial vegetation encroaching on estuarine vegetation. Sarcocornia natalensis became more abundant towards the water column. During the period of study, species richness at St Lucia ranged from 2 (Listers Point, May 2010) to 27 (Catalina Bay, February 2006). Salinity and water level fluctuation have a significant impact on the distribution of macrophytes at St Lucia during the drought. In saline areas salt marsh plants have colonized exposed shorelines and along the Eastern Shores groundwater seepage has increased macrophyte species richness. Low water levels have resulted in the exposure and desiccation of submerged macrophytes, which are replaced by macroalgae.