This investigation had three major objectives; firstly to document the estuarine fishes from several poorly studied Eastern Cape estuaries, secondly, to identify similarities and differences in the fish communities from permanently open and intermittently open estuaries, and thirdly, to establish which physico-chemical or environmental variables are responsible for the structuring of these communities. The study area incorporated 10 estuaries along a 70 km long stretch of the Eastern Cape coastline between the towns of Seafield (33° 32' 42" S, 27° 03' 05" E) in the south-east and Hamburg (33° 16' 45" S, 27° 29' 50" E) in the north-west. The systems investigated included two permanently open estuaries and eight intermittently open systems of varying sizes. Overall fish abundance and species richness in the study area revealed no significant seasonal variation. A contrast between open and closed estuaries was evident in the dominance of species from different estuarine dependence categories. Open estuaries comprised mainly category Ib, lla and IIb species, with a high proportion of category IV species. Closed estuaries were dominated by category IIa species, with few category IV species represented. Clear longitudinal trends in relative abundance were demonstrated for individual species. Margalefs species richness index for seine net catches, and a combination of the seine and gill net data, were significantly correlated with catchment size, mean annual runoff, estuarine area and linear length. Fish assemblages in the permanently open and intermittently open estuaries were significantly different (p<0.001) when analysed on a community and density basis. Similarly, the communities in large and small intermittently open estuaries differed significantly on a community (p=0.01) and density basis (p<0.001). These differences where caused by changes in abundance of the dominant estuarine resident and marine migrant species. The environmental variable that was dominant in accounting for these differences was the estuary mouth status. Estuarine resident species had smaller overall body lengths when compared with the marine migrant species. In addition, the estuarine resident species had smaller modal size classes in the closed estuaries when compared with the open estuaries. These differences may be linked to the foraging strategies of the species, as well as food availability and different levels of predation in the different estuary types. The marine migrant species did not show any trends in this respect although the closed systems had the largest individuals for all four dominant marine species. This finding may be linked to the inability of these species to breed in closed estuaries, thus channelling reproductive energy resources into somatic growth. In addition, prolonged periods of mouth closure prevent the emigration of large individuals back to the sea. Otter trawling was conducted in fiye estuaries and captured mostly demersal species. The otter trawl data confirmed the seine net community analysis, with significantly different communities identified in the permanently open and intermittently open estuaries (p=0.02), as well as in the small and large intermittently open estuaries (p=0.03). The environmental variables responsible for these community differences were mouth status and variables associated with estuarine size. The identification of estuary mouth status by this study as the most influential environmental factor is compounded by this "ariable affecting or being indicative of numerous other physico-chemical features. The large differences in the fish communities in different estuary types indicate the importance of each estuary type to various species. This should be taken into account before allowing any form of commercial fishing in these important nursery areas.

Changes in the fish communities of the Breede and Mbashe estuaries were investigated in relation to the environmental variables that influence the fish assemblages in these systems. The Breede Estuary (34° 24’21.6”S, 20° 51’ 08.2”E) occurs within the warm-temperate/cool-temperate transition-zone, while the Mbashe Estuary (32o 14' 55.4"S, 28o 54' 03.7"E) falls within the subtropical/warm-temperate transition-zone along the South African coastline. The Breede Estuary was sampled (seine and gill nets) during summer (January-March) over a period of 10 years (2002-2012), while the Mbashe Estuary was sampled (seine net) during spring (October) over a period of three years (2010-2012). The proportion of tropical fish species was higher in the Mbashe Estuary compared to the Breede Estuary, while the Breede Estuary contained a higher proportion of temperate species than the Mbashe Estuary. Although the abundance of individual species in both estuaries varied, the ranking of species in the Breede Estuary was stable over the 10 year period. Multivariate analysis showed that the fish communities within each reach (upper, middle, lower) of the Breede Estuary remained similar, regardless of year. In contrast, species composition in the Mbashe Estuary differed significantly between years mainly due to differences in the river flow regime during the study period. Environmental variables responsible for structuring the fish assemblage in each estuary differed. Salinity significantly impacted the spatial fish assemblage structure of the Breede Estuary, with most of the species recorded being associated with the more saline lower reaches. The abundance of tropical species near their distributional limit in the Breede Estuary appeared to be impacted by sea surface temperature (SST) as peak total abundance of these species coincided with the warmest SST, while the lowest total abundance coincided with the coldest annual SST during the study period. The fish assemblage structure in the Mbashe Estuary was impacted by differing freshwater input prior to sampling, with flooding negatively impacting the mean total abundance, species composition and diversity in this system. The variables that influenced the fish assemblage structure of both transition-zone estuaries will be affected by climate change in the future. These variables will, in turn, determine the composition, abundance and diversity of species within these important estuarine systems. In order to measure these impacts with any degree of understanding, long-term studies on the abiotic and biotic (including the ichthyofauna) features of these estuaries are required to interpret climate change trends.

Phylogeographic patterns of coastal organisms with different life histories and breeding strategies may reveal patterns not consistent with the current delineation of the biogeographic provinces around South Africa. The subdivision of the South African coastline into these three main climatological or biogeographic regions: namely the cool temperate west coast, the warm temperate south coast and the subtropical east coast, is based on average seawater temperatures and hydrological conditions. Genealogies of two estuarine fish species Atherina breviceps, a marine breeder, and Gilchristella aestuaria, an estuarine spawner, were reconstructed using mitochondrial DNA (mtDNA) control region sequences. The study comprised two components, an assessment of a small dataset of both fish species to compare their population structure along the South African coastline and a more comprehensive investigation of the phylogeography of G. aestuaria collected from 21 estuaries around the coast. The comparative study of A. breviceps and G. aestuaria indicate different population distribution patterns along the South African coastline. Results of the A. breviceps analysis demonstrate substantial gene flow due to the random mixing of alleles, while the comparative G. aestuaria dataset indicates a more structured population and considerably less gene flow. The G. aestuaria population demonstrates geographic separation into four groups, namely the west coast (Great Berg), Bot (south coast), Seekoei (south coast) and east coast (Bushmans, Kasouga and Cefane). Results from the larger G. aestuaria dataset indicate that the phylogeographic patterns observed during this study do not conform to existing biogeographic boundaries along the southern African coastline. The delineation identified during this study between the warm temperate and subtropical regions is further south than originally perceived and this southward extension can be ascribed to the prevailing hydrology. The life history patterns and ecology of these two estuarine fish species appears key to understanding their population structure. These factors interact with environmental characteristics such as physical oceanography and the distribution of estuaries (along the coastline) to explain the observed distribution patterns and population structure of A. breviceps and G. aestuaria.

The biogeography and community structure of the fishes of South African estuaries was investigated. In all, 109 systems were examined representing two broad types: temporarily closed and permanently open estuaries. Multivariate analyses of the fish communities identified three biogeographic regions. A cool-temperate region extended along the west and southwest coasts; a warmtemperate zone stretched along the south, southeast and east coasts and a subtropical region occurred along the east coast. The boundaries of these biogeographic regions were also delineated. The general physico-chemical characteristics of the estuaries within the three biogeographic regions also reflected regional differences in climate, rainfall and ocean conditions. Estuarine temperatures followed the trend for marine coastal waters, decreasing from subtropical estuaries toward cool-temperate systems. The low rainfall and runoff in the warm-temperate region together with high evaporation rates and strong seawater input resulted in higher salinities in these estuaries. These factors also accounted for the predominantly clearer waters in warm-temperate estuaries. The estuaries in the three biogeographic regions were also shown to contain somewhat distinctive fish assemblages. Temperature and salinity appeared to be the two main factors affecting the distribution and abundance of fishes in South African estuaries. Subtropical systems were characterised by fishes mostly of tropical origin as well as certain south coast endemic species. Warm-temperate estuaries were dominated by endemic taxa with some tropical species also present. The fish fauna of cooltemperate estuaries mostly comprised south coast endemic species with cosmopolitan and temperate taxa also present. Certain functional components of the ichthyofauna also exhibited slight differences between regions. Freshwater fishes were a major component of closed subtropical estuaries while estuarine resident species were more abundant in warm-temperate estuaries. Overall, estuarine-dependent marine species dominated the fish fauna of the estuaries in all biogeographic regions, signifying that South African estuaries perform a vital nursery function for this group of fishes. Slight differences were also apparent in the trophic structure of the fishes; these were related to environmental differences between regions. Zooplanktivores and fishes that feed on aquatic macrophytes/invertebrates assumed a relatively higher importance in warm-temperate systems. Overall, detritivores dominated the estuarine fish fauna in all regions, indicating that detritus forms the main energy source in South African estuaries.

Ichthyoplankton dynamics in the permanently open Kowie Estuary, in the warm temperate region of South Africa was investigated. The composition, abundance, distribution and seasonality of larval fishes were studied over a two year period between 2004 and 2006. Additionally, tidal exchange of ichthyoplankton and the use of frontal zones in the mouth region of the estuary were also explored between 2008 and 2009. Temporal and spatial trends in occurrence of larval fishes within the estuary and associated marina were obtained from data collected seasonally using boat-based plankton netting at 14 sampling stations along the length of the estuary. A total of 11 128 larval fishes were collected, representing 23 families and 38 taxa. Clupeidae and Gobiidae were the dominant fish families, contributing 47.0 % and 24.7 % respectively to the total catch. Estuarine resident species dominated the overall catch (91 %). A notable absence of older stage larvae and early juveniles characterised the artificial channels of the marina and estuary mouth region. This was attributed to the absence of a shallow, marginal water habitat typical of successful estuarine nursery areas. Tidal exchange of larval fishes was investigated in the Kowie Estuary using a new technique. A set of drifting light traps were set repetitively on the ebb and flood tide every second night for two consecutive 14 day periods during the peak estuarine recruitment period. A total of 553 larval fishes were caught during the study, representing nine families and 26 species. Blenniidae and Clupeidae dominated the catches. Family and species occurrence changed with tide state. Species richness (d) and diversity (H’) varied with tide and was highest on flood tides. Estuary-dependent species, such as Omobranchus woodii were more dominant on flood tides, whilst larvae of marine-spawned species, such as Sardinops sagax, were dominant on the ebb tide. Light trap catches yielded a different composition in terms of development stage / size and species, when compared to towed net studies. Towed plankton nets were again used to study the shear fronts that characterise the mouth region of the canalised Kowie Estuary. It was hypothesised that the convergence zone of the front provides feeding opportunities for ichthyoplankton. Ichthyoplankton, zooplankton and phytoplankton was collected from within and immediately outside of the convergence zone during frontal conditions. Species specific distribution trends emerged from this study. Postflexion larvae and early juvenile stages of the estuary dependent Mugilidae were only present in the foam line of the convergence zones. Some known predators of ichthyoplankton were also present in slightly higher numbers in the convergence zone (isopods) while other predators such as mysid shrimps, chaetognaths and cnidarians were more abundant out of the convergence zone. It appears that these zones may provide access to temporary food patches in the lower estuary but will be accompanied by a trade-off with increased isopod predators. The Kowie Estuary is a heavily impacted system and lack of adequate freshwater supply; artificial channelling and pollution ultimately have a negative impact of the success of this system as a nursery area. Rehabilitation of marginal areas in the lower estuary and marina is suggested as remedial action to re-establish the integrity of the nursery function this system could offer.

Early stage fishes, namely larvae and early juveniles, were collected from 12 estuaries and associated habitats in the warm temperate region of South Africa between July 1998 and December 2000. This study served to provide new information and expand on existing knowledge of early stage fish assemblages associated with various types of Eastern Cape estuaries. A total of 65 536 predominantly postflexion fish larvae were collected. Together with early juveniles, taxa comprised 72 species from 25 teleost fish families. Surf zones associated with two intermittently open estuaries showed that estuary-dependent marine species predominated in this zone. Early stage fishes responded positively during natural estuary opening events and concentrated along the estuary outflow plume, suggesting that cueing from estuary and/or river water may be taking place. A habitat study in the Swartkops Estuary, using light traps, showed that newly recruited larval fishes concentrated along the margins of the estuary and unlike their older juvenile counterparts, were poorly represented in eelgrass beds. A multi-estuary comparison, including seven permanently open and five intermittently open estuaries, indicated that early stage fish assemblages were more diverse than indicated by past investigations. Early stage fishes were also shown to concentrate in the mesohaline regions of these estuaries. Studies of estuaries with altered freshwater flow regimes were also included in the research. A regulated release of dam water in the euhaline Kromme Estuary failed to induce a cueing response from estuary-dependent marine fish larvae. This project showed that large amounts of freshwater are required to reverse the negative effects of river impoundments. The release study did show that estuary-resident fishes were sensitive to small natural pulses of freshwater and responded by spawning. However, excessive river supply through an inter-basin water transfer scheme was shown to have a flushing effect on the larvae and early juveniles of the estuary-resident Gilchristella aestuaria in the upper reaches of the Great Fish Estuary. This effect was evident in comparisons with the freshwater starved Kariega Estuary where concentrations of G. aestuaria, a species usually more abundant in freshwater rich estuaries, were considerably higher. This finding suggests that freshwater minima and maxima be considered when assessing and managing estuarine systems.

The spatial and temporal pattern of ichthyofaunal community composition in relation to selected physico-chemical (temperature and salinity) and biological variables (chlorophyll-a and zooplankton) was investigated at ten stations in the temperate temporarily open/closed Kasouga estuary. In addition, the food web structure in the estuary was investigated using stable carbon isotope analysis. Results of the 5 metre seine net survey indicated that ichthyofaunal composition and biomass in the Kasouga estuary was largely determined by seasonality and mouth condition. Maximum abundance and biomass of ichthyofauna was recorded during summer or during those periods when overtopping occurred. Overtopping coincided with the recruitment of marine estuarine dependant species, which dominated the catches both numerically and in biomass. The recruitment of these species resulted in an increase in diversity of the ichthyofaunal community. There were no significant spatial patterns in the distribution of smaller ichthyofauna (<50mm SL) identified in Bray-Curtis similarity matrices using cluster analysis (Primer 5 v5.2.4). Spearman’s correlation analysis revealed that there were no significant correlations between abundance and biomass of ichthyofauna and selected physico-chemical and biological variables other than salinity (P>0.05 in all other cases). There were two distinct spatial patterns in the distribution of the larger ichthyofauna (>50mm SL). These corresponded to a grouping associated with the mouth region and a grouping associated with the remaining regions of the estuary. Stable isotope analysis indicated that the primary source of carbon utilised by the ichthyofauna of the Kasouga estuary was derived from the channel, most likely microphytobenthic algae. The contributions of the riparian and salt marsh vegetation to the total carbon flow appear to be minimal.

The Mngazana and Mngazi estuaries are situated just south of Port St. Johns close to the biogeographical boundary between the warm temperate and subtropical zones along the east coast of Southern Africa. The Mngazana estuary is a permanently open estuary with three species of mangrove. The Mngazi estuary is a temporarily open/closed system. The ichthyofauna was sampled with seine nets and gillnets during June 2005, August 2005, November 2005, February 2006 and April 2006. The fish community structure was significantly different between the two estuaries with the differences being especially noticeable in the larger fish sampled with gillnets. There were significant differences in the fish community sampled with the seine net on both spatial and temporal scales in both of the estuaries. Certain warm temperate species were less abundant and certain subtropical species were more abundant at the Mngazana estuary than they were during a study conducted in 1975. Stomach content analysis revealed that most species had similar diets in the two estuaries with the only differences occurring among benthic feeding species. The diet of sub-adult piscivores comprised of a large proportion of penaeid prawns while the juveniles feed mainly on mysids. The zooplanktivorous fish feed mainly on copepods and mysids with the proportions varying between the species. Benthic feeding fishes showed the greatest variability in diet with plant material, detritus, crabs and copepods being the main food sources. Stable isotopes revealed that particulate organic matter and microphytobenthos were the most important carbon sources to fish in the Mngazi estuary. In the Mngazana estuary a combination of mangrove material, detritus, particulate organic matter and Zostera material were the most important carbon sources. The importance of each of these sources did, however, vary greatly between the different trophic guilds of the fish in the Mngazana estuary. The distribution of certain fish species was investigated in relation to physical parameters (temperature, salinity, turbidity and depth) and biological parameters (prey and predators) in the environment. It was found that most small fish (< 100 mm SL) were strongly correlated with turbidity where-as they showed weak correlations with their prey. Sub-adult piscivores fell into two groups, i.e. those that could tolerate turbid water and those that were only found in clear water. The group that also occurred in turbid water showed very strong correlations with their prey but the clear water group did not. It would appear that the small and thus vulnerable fish seemed to occur in areas that offered them protection rather than areas where their food supply is most abundant, where-as the piscivores were more influenced by prey distribution, as long as the physical conditions were tolerable to them.

Estuaries serve as nursery areas for a large number of estuary-associated fish species. Some of these taxa also use river catchments as nursery areas. During the upstream migration of this latter group, the juveniles are prone to predation by native and alien predatory fish inhabiting the system. The rate of invasion of ecosystems by alien organisms can be directly linked to anthropogenic influences, including both intentional and unintentional introductions by alien organisms into new regions. The largemouth bass, Micropterus salmoides, is a facultative piscivorous fish that has been successfully introduced worldwide for the main purpose of sport fishing. Where introduced, it has been found to negatively impact native fish and invertebrate species through predation, competitive exclusion and displacement of indigenous fish species. The aim of this thesis was to investigate the predatory impact of largemouth bass on the estuary-associated Cape moony Monodactylus falciformis, Cape stumpnose Rhabdosargus holubi and freshwater mullet Myxus capensis in the lower Kowie River of the Eastern Cape Province, South Africa. A combination of approaches was employed during this study. Stomach contents, stable isotopes and fatty acid analyses were employed for the reconstruction of the diet of largemouth bass. Acoustic telemetry was used to elucidate largemouth bass movements, particularly their ability to enter the upper reaches of the Kowie Estuary. Stomach contents and stable isotopes analyses showed that M. salmoides exhibit an ontogenic shift in diet, with small and medium sized individuals consuming the higher proportion of fish prey, while large sized individuals mostly consumed invertebrates such as crabs (Potamonautes sidneyi) and Odonata larvae, while consuming only a small proportion of estuary-associated fish. Fatty acid analysis only showed a direct connection between the fatty acid profiles of largemouth bass and those of M. capensis and M. falciformis. The acoustic telemetry results indicated that some M. salmoides individuals periodically move into the upper reaches of the estuary following river flood events. The results obtained from all these approaches highlight the risk posed by largemouth bass introductions on indigenous fish species, particularly those that enter the areas occupied by these top predators.

Long-term interannual changes in richness, abundance, diversity and structure of the fish community in the temporarily open/closed East Kleinemonde Estuary, Eastern Cape, are described and the recruitment success of two estuary-dependent marine species assessed. In addition, laboratory experiments were conducted to assess the possible role of olfaction in the recruitment process of an estuary-dependent marine fish species. Multivariate analyses of the annual marine fish communites identified two distinct groups with more species recorded during years that succeeded spring (September to November) mouth opening events than in years following no mouth opening events in spring. Interannual community stability (IMD) and seriation (IMS) also increased from the ‘other’ to the ‘spring’ years. These results highlight the importance of the timing of mouth opening to the marine fish community in a temporarily open/closed estuary. This study also made use of long-term records of daily mouth state and linked them to the recruitment of distinct year-class cohorts in two spardis with contrasting lifehistory characteristics. Lithognathus lithognathus only recruited into the estuary in years when the mouth opened between late August and January. This was linked to the limited spawning season of this species and its inability to enter closed estuaries via wave overwash events. In contrast, recruitment by Rhabdosargus holubi juveniles appeared to be uninterrupted and was not determined by the seasonality of mouth opening. This species dominates the marine-spawning component of the East Kleinemonde Estuary and its success is attributed to an extended spawning season and its ability to recruit into estuaries during both overwash and open mouth conditions. Attraction of postflexion Rhabdosargus holubi larvae to estuary, surf zone and river water was also measured using a rectangular choice chamber. In two sets of experiments, conducted during peak recruitment periods, larvae from both the surf zone and estuary mouth region selected estuary water with a significantly higher frequency than sea water. Larvae collected in the mouth region showed a stronger preference for river water than those collected in the surf zone, thus suggesting that these fish are more attracted to freshwater influenced nursery areas once they have entered the estuary than those in the surf zone. Larvae collected in the marine environment also selected surf zone water with significantly higher frequencies than estuary water or offshore sea water, thus confirming the importance of the surf zone as an interim nursery area for postflexion R. holubi.