River flow is important in controlling phytoplankton distribution in estuaries. Data on the effect of river inflow on phytoplankton distribution patterns in temporarily open/closed estuaries is lacking. This study investigated the influence of river inflow on size-fractionated phytoplankton biomass (Chl a), community composition and environmental parameters measured monthly over three years in two temporarily open/closed estuaries in the Eastern Cape, South Africa. A once-off primary production study over an annual cycle was completed in the Van Stadens and Maitland estuaries. The study monitored physical, chemical and biological characteristics in both estuaries to examine the effects of changes in environmental factors and river inflow. Daily sampling of physico-chemical and biological variables from river to sea was carried out in the Van Stadens to investigate short-time scale effects of changes in environmental factors and river inflow on the phytoplankton biomass. Five and three stations in the main channel of the Van Stadens and Maitland estuaries respectively were sampled at 0.5 m below the water surface and 0.5 m above the sediment surface for biological and chemical variables and at the surface, 0.25 m and every 0.5 m thereafter for physical parameters. Five stations adjacent to the main channel along the estuary were monitored for groundwater macronutrient concentrations and five additional sites located within the upper catchment of the Van Stadens River were sampled on a quarterly basis over two years. Both estuaries were characterised by distinct hydrological conditions, an overwash, an open, a closed and a semi-closed mouth phase. Flooding in the Maitland and Van Stadens estuaries in 2001 and 2002 caused sediment scour, altered channel morphology and brought about breaching of the mouth. Flood driven mouth-breaching events occurred three and four times in each of the estuaries during the study. The mouth stayed open 20 – 25 percent and was closed 60 – 65 percent of the time. In the Van Stadens the closed overwash mouth condition occurred approximately 10 – 20 percent of the time while in the Maitland it occurred less with the semi-closed mouth condition occurring 10 – 20 percent of the time. Incidents related to mouth opening not associated with strong river floods occurred approximately 10 – 15 percent of the time, although in the Maitland a semi-closed mouth state persisted more frequently than in the Van Stadens Estuary. During flooding events salinity dropped to low levels (< 5 psu) but soon recovered to brackish conditions when river flow was reduced and marine water penetrated deep upstream. Reduction in river flow combined with marine sediment deposition resulted in the closure of the mouth. During closed mouth conditions strong onshore storm surges and spring high tides introduced marine water through overwash that kept salinity high. In both estuaries salinity showed a negative correlation with rainfall (R2 = 0.12), indicative of the strong influence of marine overwash that kept salinity high thus masking the influence of freshwater. High rainfall in the Van Stadens Estuary caused high levels of turbidity that reduced light penetration at depth. Light attenuation was positively correlated with the high rainfall (R 2 = 0.26) suggesting that increased turbidity was linked to rainfall induced discharge. In contrast, in the Maitland Estuary light attenuation did not show any correlation with increased rainfall possibly because of the reduced water depth and increased euphotic zone following the floods in 2002. High river inflow introduced macronutrients in both estuaries such that dissolved inorganic phosphates (DIP) and dissolved inorganic nitrogen (DIN) concentrations in the Van Stadens Estuary were strongly correlated with rainfall (R2 = 0.78 and 0.57 respectively). In the Maitland Estuary DIP and DIN concentrations remained significantly higher (p < 0.05) compared to that in the Van Stadens suggesting that the Maitland catchment contributed greater nutrient input into the estuary and may be associated with farming activities. Phytoplankton chlorophyll a (Chl a) ranged from 0.8 – 13.9 μg L-1 in the Van Stadens and in the Maitland Estuary from 5.3 – 138 μg L-1 during the 3-year study. During the open mouth condition Chl a biomass and primary production ranged from 5.4 – 52.9 μg Chl a L-1 and 1.2 – 11.7 mg C m-2 d-1 in the Maitland and in the Van Stadens from 1.6 – 9.8 μg Chl a L-1 and 1.2 - 14 mg C m-2 d-1 respectively. Maximum annual primary production in the Maitland and Van Stadens estuaries was 8.8 and 5.1 g C m-2 y-1 respectively. When the mouth was open in the Van Stadens Estuary the microphytoplankton (> 20 μm) accounted for > 65 percent of the Chl a, whereas during closed mouth conditions they accounted for about 55 percent of the Chl a biomass. Chlorophytes became the dominant taxon in the dry summer months but were replaced by cryptophytes and dinoflagellates during the wet season. When nutrient concentrations were low during low flow conditions in the Van Stadens Estuary mixotrophic microphytoplankton became an important fraction of the water column together with phototrophic dinoflagellates and cryptophytes. In the Maitland large sized chlorophytes were the dominant taxa in late spring and summer seasons and made up more than 80 percent of the cell numbers. In the Maitland before the floods in 2002 cyanophytes were the dominant group in late spring contributing more than 75 percent in cell abundance. Data from the short-term study in the Van Stadens Estuary showed similarities and differences in the Chl a response to increased river inflow. High river inflow initially reduced Chl a biomass followed by a recovery period of a couple of days compared to a 8 – 10 week recovery period in studies monitored over seasonal and annual temporal scales. The responses may be dissimilar but help to illustrate that there are similar response patterns to environmental forcing necessary to support phytoplankton biomass at different temporal scales. This study has demonstrated that flooding events caused by strong river flow cause breaching of the mouth, a reduction in salinity and marked nutrient input. Although the causes of flooding can be similar in both estuaries the resultant effects are varied and can alter the ability of the estuary to retain water. This study was able to demonstrate that the supply of macronutrients from the catchment was strongly correlated with rainfall (R2 = 0.67) and that phytoplankton growth mainly depended on an allochthonous source of macronutrients although internal supplies could be critical at times in controlling microalgal biomass.

The Great Brak temporarily open/closed estuary was subjected to a drought during the spring and summer of 2009/2010 resulting in the mouth remaining closed for a prolonged period. According to the Great Brak Estuary management programme, the mouth of the estuary had to be open for a total of 308 days during spring and summer of 2009/2010, respectively, but was closed for almost the entire two years (693 days). The aim of this study was to assess monthly changes in the abiotic characteristics (salinity, temperature, oxygen, pH and nutrients) and the biotic responses of phytoplankton and macroalgae; identify sources of nutrient input into the estuary and determine the response of the salt marsh to water level and salinity changes. The results indicated that physico-chemical parameters were similar to that previously recorded during the closed mouth condition. However mouth closure combined with elevated nutrient concentrations led to a shift from rooted submerged macrophytes to one where either microalgae or macroalgae were dominant. Soluble reactive phosphorus concentrations were significantly higher in bottom compared with surface waters. There was a significant negative correlation with SRP and dissolved oxygen for the sampling period indicating potential release of phosphorus from the sediment during closed mouth conditions. Microalgal biomass increased in response to remineralised nutrients and freshwater pulses. Flagellates were the dominant microalgal group (21718 ± 3336 cells m l-1, p < 0.05) because of their morphological ability to migrate vertically within the water column. The macroalgal cover was highest during the closed mouth state but only during winter (August 2010) when temperatures were below 20 oC. Five major point sources of nutrient input into the Great Brak Estuary were identified during rainfall periods. Point sources 4 and 5 in the upper reaches of the estuary had the highest DIN input whereas point source 3 in the middle reaches of the estuary had the highest DIP input. As a result of the drought and low water level, the salt marsh was never inundated for longer than 3 months. Die-back of Sarcocornia decumbens (r 2= -0.62, p < 0.05) was related to smothering by dead macroalgae whereas dieback of Sporobolus virginicus was related to decreasing nutrient (r2 = 0.59, p < 0.05) and salinity (r2 = 0.55, p < 0.05) levels. The physico-chemical characteristics alone did not convey the true health status of the Great Brak Estuary for the duration of the sampling (April 2010-April 2011). The study showed that microalgae and macroalgae are valuable indicators of the status of the estuary. Therefore it is suggested that bio-indicators are incorporated into the management/monitoring plan in order to assist in improving the health assessment of the Great Brak Estuary.

This thesis presents the first intensive community-level investigation of the mesozooplankton from a biogeographical transition zone estuary. The Mgazana Estuary is located along a rural, semi-undeveloped part of South Africa’s east coast, believed to represent a transition zone between the subtropical and warm-temperate biogeographical zones. The research represented in this thesis involves data collected over a five year period between 2002 and 2006, with additional data collection made in 2008. The study focussed on five areas of investigation, the first of which investigated the physico-chemical dynamics of the Mgazana Estuary. The Mgazana Estuary exhibited marked vertical, horizontal and regional structures in the hydrological environment. Prominent vertical and horizontal stratification characterised summer months. A substantial turbidity front was observed in the lower estuary during summer and winter. The upper estuary was marked by considerable variation in multiple variables but especially salinity. These structures appeared to have shifted in position over the horizontal plane, which was attributed to variation in freshwater flow. The second study focused on the spatial dynamics of mesozooplankton in the Mgazana Estuary. The zooplankton was rich and in terms of composition typical of mangrove systems. The Copepoda were dominant, numerically and in terms of taxonomic representation. Calanoids Acartiella natalensis and Pseudodiaptomus hessei characterised middle and upper reaches in summer and mostly upper reaches in winter. On community level, a highly structured assemblage arrangement was observed during summer and winter months. These trends were further scrutinised under the theoretical framework of ecological boundaries. In so doing, an agreeable spatial association emerged between specific assemblages and their environments. These trends were concluded to reflect ecoclinal as well as ecotonal properties, the latter describing interactions over narrow spatial bands of marked changes in turbidity. The third study investigated flooding events as short-lived extreme meteorological events and the influence on zooplankton. Within this regard, second-stage multivariate statistics was used to assess year-to-year variability in assemblage structures on whole-system and regional scales. The impact of two major flooding events that flushed the estuary some days prior to sampling could clearly be elucidated. Flooding emerged as a significant source of inter-annual variability in the zooplankton of the Mgazana Estuary. Second-stage multivariate analysis proved to be an effective analytical strategy for investigating inter-annual variability in species assemblage structures. Results from the preceding study prompted a detailed investigation into the spatio-temporal dynamics of Acartiella natalensis, the most important zooplankton species of the system aimed at elucidating flood responses. Acartiella natalensis showed indication of temporal arrest in association with flooding events in a similar fashion as is observed in seasonal variation trends in estuaries towards its geographical distribution limit south of the study area. It was concluded that A. natalensis was severely affected by floods and the possibility exist for entrainment of entire populations from the estuary during flooding events. The final study tested the hypothesis of post-flood propagation from a resting egg bank in the sediments of the Mgazana Estuary. Preliminary data revealed that numerous eggs were present in the sediments. Nauplii hatched from eggs under laboratory conditions were identified as belonging to the family Acartiidae. The preliminary mode of diapause is presented as a schematic model, emphasising the role of freshwater flow and specific environmental variables. This was the first discovery of resting eggs from a subtropical estuary from South Africa. It is hoped that the findings of this study would give rise to new research initiatives investigating the importance of resting stages in estuarine and coastal Copepoda species and the role such reproductive strategies may play in estuarine functioning.

An estuary is the last stage of a river. It is where the river meets the sea. Estuaries are one of the most significant features of the South African coastline. In recent years, South Africa has witnessed an increase in the demand for freshwater for both industrial and domestic purposes. At the same time, there has been a gradual deterioration of river systems and their catchments. To add to this, there has been a gradual reduction in the amount of recorded rainfall, which is the primary source of freshwater for rivers. This has resulted in decreased freshwater inflow into estuaries, a situation which poses a serious threat to the biological functioning of these estuaries and the services rendered to its recreational users. A deterioration of estuary services reduces the yield for subsistence households and their appeal for recration. This study uses the contingent valuation method as its primary methodology to elicit users' willingness-to-pay to reduce the negative impacts of reduced freshwater inflow into selected western and southern Cape estuaries. Eight estuaries were selected for this study; the Breede, Duiwenhoks, Great Berg, Kleinemond West, Mhlathuze, Swartvlei and Olifants estuaries. The contingent valuation (CV) method is widely used for studies of this nature because of its ability to capture active, passive and non-use values. The CV method involves directly asking people how much they would be willing to pay for specific environmental services. In this case, users were asked what they would be willing to pay to sustain freshwater inflows into selected estuaries in order to prevent the negative impacts of reduced inflows. The travel cost method (TCM) was uesed to generate an alternative comparative set of values for the purposes of convergence testing. This is because convergence testing is highly desirable as a validity test for CV estimates.

There are about 259 estuaries in South Africa that can be classified as “functioning” and their “health” status is directly related to the quantity and quality of freshwater that flows into them. Many of South Africa’s estuaries have become smaller due to a steady decrease in the amount of freshwater that flows into them. This reduction in freshwater inflows decreases their ecological functioning and undermines the recreational activities and subsistence services available from them. The National Water Act (ACT No. 36 of 1998) recognises the right of the environment to water, but a large amount of data is still needed to make management decisions on the allocation of freshwater. The objective of this research was to contribute to the management of the allocation of freshwater in the catchment areas of the Bira, Bushmans, Kasouga, Keiskamma, Kleinemond East, Nahoon and Tyolomnqa rivers by determining the recreational value of the freshwater flowing into their estuaries. This recreational value was established using the contingent valuation method. The contingent valuation method (CVM) is a technique to establish the value of a good (or service) that is not bought or sold in an actual market. This technique is frequently applied in the valuation of environmental goods, e.g. the freshwater that flows into an estuary. The CVM establishes the economic value 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 then aggregated to establish a total willingness to pay (TWTP) for the population of the users of the environmental good. The hypothetical project presented in this study is that of an increase of freshwater inflows, that would prevent (bring about) predetermined changes in environmental services provided by the selected seven estuaries.

The primary aim of this study was to investigate the population dynamics of the fishes associated with a small (17.5 hectares) temporarily open/closed estuary on the south east coast of South Africa. The results are based on the findings of an intensive sampling programme conducted over a period of four years in the East Kleinemonde estuary (33° 32' S : 27° 03' E). By adopting a quantitative approach, this study addresses the need for information on estuarine-associated fish population sizes, standing stock (biomass) estimates and productivity. The ichthyoplankton assemblage in the surf zone adjacent to the mouth of the estuary was dominated by postflexion larvae representing at least 21 taxa in 14 families. Rhabdosargus holubi of sizes ranging between 9 mm and 21 mm BL was the most abundant species with a mean density of 7.3 individuals per 100 m'. This species, which accounted for 77.6% of the catch composition, was recorded throughout the year but revealed a distinct peak in abundance in spring (August - September). The ichthyofaunal community within the East Kleinemonde estuary was dominated by juvenile marine-spawning species and typical of a warm temperate southern African estuary. A total of 30 species in 17 families was recorded, including the endangered estuarine pipefish Syngnathus watermeyeri. Multivariate analyses (classification and ordination) of the catch assemblages revealed a high degree of similarity (> 70%) throughout the estuary, with two distinct groups being identified on the basis of substratum type. The sampling stations near the mouth with a sandy substratum were distinguished from all other sampling sites in the estuary. The dominant estuarine-spawning species were represented by all life-history stages, suggesting that they bred successfully in the estuary. This group was numerically and gravimetrically dominated by the two zooplanktivorous shoaling species Gilchristella aestuaria and Atherina breviceps with density extrapolated population size estimates of 420 973 and 198 275 individuals, and biomass estimates of 1.6 and 0.6 g m⁻² respectively. The total population size of all estuarine-spawning species with a mean biomass 00.4 g m⁻² was estimated at 754 217 individuals. Population size estimates of the marine-spawning species were calculated using data obtained from three independent mark-recapture experiments. The assumptions for the mark-recapture analyses were adequately met and it was concluded that the techniques provided reliable estimates of population size. However, estimates obtained from density extrapolation revealed enormous variability and were considered to be unreliable. The total population size was estimated at 63 342, 18 592 and 13 5 192 during the three mark-recapture experiments respectively. The numerically dominant species during all three experiments was Rhabdosargus holubi. Biomass production of the marine-spawning species was evaluated over a 123 day census period when population sizes and estimates of growth rates were known. Productivity for all fishes with a standing stock of 26.2 g m⁻² was calculated at 4.5 g m⁻² month01 Rhabdosargus holubi accounted for more than 75% of the total marine fish productivity. This study draws attention to the success of Rhabdosargus holubi in the East Kleinemonde estuary, which is ascribed to aspects of its biology. These include an extended breeding season, the ability to recruit into the estuary under adverse open mouth conditions and its omnivorous food habits. The dominance of this migratory species suggests that it plays an important role in the transfer of energy to the coastal marine environment when the mouth of the East Kleinemonde estuary opens. Predation by birds and a dominant piscivorous fish (Lichia amia) was quantitatively assessed over a period of two years. Monthly food consumption by all piscivorous birds revealed large temporal variability, ranging from 32 to 466 kg month-I An unusual invasion of Cape cormorants during the winter of 1994 accounted for large scale mortality (2246 kg of fish) over a relatively short period. The predatory impact of this episodic event was reflected in the findings of the fish mark-recapture experiments, which revealed a 70% reduction in the total population of marine-spawning fishes (above a certain minimum size) in the estuary subsequent to this invasion. Monthly food consumption by the Lichia amia population in the estuary was calculated at 68 and 58 kg month-I for two distinct time periods when the population size was known. These findings suggest that this species is the top piscivorous predator in the East Kleinemonde estuary. Finally, the findings of this study highlight the temporal variability of fish populations within a single estuary. It is suggested that predation and estuary mouth conditions are the main factors influencing the abundance (and its variability) of individual species in the East Kleinemonde estuary.

The ichthyofauna of three small Natal estuaries, the Mhlanga, Damba and Zotsha was sampled over a period of two years. A total of 68 kinds of fishes representing 24 families, 39 genera and 56 species were captured during this study. Forty seven kinds of fishes were recorded in the Mhlanga of which Gilchristella aestuaria,Oreochromis mossambicus, Valamugil cunnesius, Valamugil sp. and juvenile mugilids numerically dominated. In terms of biomass, O. mossambicus, V. cunnesius, Liza alata, Myxus capensis and Mugil cephalus dominated the ichthyofauna of the Mhlanga. In the Damba, 24 kinds of fishes were recorded. The most abundant fishes captured were Glossogobius callidus, M. capensis and O. mossambicus. M. capensis, M. cephalus, O. mossambicus and G. callidus dominated the fish biomass captured in the Damba. A total of 56 kinds of fishes were recorded in the Zotsha during this study. The ichthyofauna of the Zotsha was numerically dominated by juvenile mugilids, G. aestuaria, O. mossambicus, Rhabdosargus holubi, Terapon jarbua, Ambassis productus and G. callidus. The species which dominated the fish biomass in the Zotsha were O. mossambicus, L. alata, Valamugil robustus, Valamugil buchanani, M. capensis, M. cephalus and V. cunnesius. Classifying the species captured according to whether they were resident estuarine species, freshwater species, estuarine-dependent marine species and marine species revealed that the first three groups were all well represented in the systems. The only system in which marine species made any significant contribution to the ichthyofauna was the Zotsha. Oreochromis mossambicus was the dominant freshwater species in all three estuaries during this study. Gilchristella aestuaria and Glossogobius callidus were the principal estuarine species in the Mhlanga and the Damba respectively. Both G. aestuaria and G. callidus were the dominant estuarine species captured in the Zotsha. The principal estuarine-dependent marine fishes captured in the Mhlanga were V. cunnesius, Valamugil sp., juvenile mugilids, M. capensis, M. cephalus and L. alata. In the Damba, M. capensis and M. cephalus were the dominant estuarine-dependent marine species and in the Zotsha juvenile mugilids, R. holubi, T. jarbua, A . productus, M. capensis, V. cunnesius, V. robustus, M. cephalus and L. alata predominated. The results of this study indicate that the estuaries are dominated at different periods by different assemblages of fishes. This is linked to the spawning and migration patterns of the various species as well as the hydrological regime of each estuary. During the winter these systems are normally closed with relatively deep waters and high food resource and habitat availability. Freshwater and estuarine species mainly inhabit the upper reaches of the systems while estuarine-dependent marine species mainly occupy the middle and lower reaches and dominate the fish community. When these systems open with the onset of the spring/summer rains, adult and sub-adult estuarine-dependent marine species emigrate to the marine environment and juveniles begin recruiting into the systems. Spring is also the peak breeding period of resident estuarine and freshwater species, resulting in an increase in the contribution of these fishes to the overall population during this period. When closed estuaries open many of them drain and this results in the fishes concentrating in the lower reaches of the system where moderate water depths are present, thus further contributing to an increase in the proportion of freshwater and estuarine species in this region. The breaching of closed estuaries also results in a slump in food resources and habitat availability. Competition and possible increased vulnerability to avian predation (due to the shallow nature of the systems), may contribute to a decrease in the proportion of estuarine and freshwater species in summer. The prolonged spawning and recruitment of 0+ juveniles of estuarine-dependent marine species results in an increase in the proportion of these fishes present in the estuaries during summer. In autumn, these systems normally close, water levels rise and available food resources and habitat increase. This allows the redistribution of freshwater and estuarine species upstream, leaving estuarine-dependent marine species to dominate the middle and lower reaches. Although temporarily open/closed estuaries along the Natal coast may not be as diverse as permanently open estuaries in terms of their ichthyofauna, their importance must not be underestimated since by providing a continuous sequence of sheltered habitats along the coast they may contribute significantly to the viability of estuarine-dependent marine fish stocks.

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.

Water quality characteristics of the heavily urbanised and industrialised Swartkops River catchment in the Eastern Cape has been the focus of several studies since the 1970s. Overloaded and poorly maintained wastewater treatment works (WWTW), polluted stormwater runoff and solid waste have had a negative impact on the water quality status of the Swartkops River and estuary. Past studies have revealed that a distinct relationship exists between land use activities and the water quality of the Swartkops Estuary, which in turn has raised concerns pertaining to the ecological, economic, recreational, and cultural value of the estuaryThe Swartkops Estuary has a Present Ecological State (PES) of Category D(1) and a Recommended Ecological Category (REC)(2) of a C (Van Niekerk et al., 2014). It is known that effective management of anthropogenic impacts on coastal systems requires a thorough understanding of the system’s biological responses to wastewater discharges and to hydrologic changes. For this reason, the objective of this study was to determine the current water quality status of the Swartkops Estuary, and to gain greater insight into factors controlling eutrophication. This was important as outdated water quality information was used in the Swartkops Integrated Environmental Management Plan (Enviro-Fish Africa, 2011) due to a lack of current data. To determine the current water quality status of the Swartkops Estuary the present study investigated spatial and temporal variability in physico-chemical parameters, nutrients, phytoplankton biomass and community composition, faecal bacteria, and “where possible” related this to historical water quality data. In general, points of entry into the estuary were investigated for their impact on nutrient enrichment and the bacteriological status of the estuary. Water quality surveys were completed in September 2012, November 2012, February 2013, May 2013 and August 2013The present study found evidence to suggest that water is not flushed as efficiently from the estuary as was previously the case, and that the natural hydrology of the estuary has been modified. These changes appear to be the effect of large volumes of wastewater discharges from the wastewater treatment works (WWTW), which has led to the additional stresses of increased vertical stratification and reduced vertical mixing. A build-up of dissolved inorganic nutrients has given rise to persistent eutrophic conditions and phytoplankton blooms occurring from the middle reaches to the tidal limit of the estuary. These findings were associated with a generally well oxygenated estuary; however, bottom water hypoxic conditions were recorded in the upper reaches of the estuary on two occasions and were generally associated with bloom.forming flagellates. Elevated concentrations of inorganic nutrients stimulated phytoplankton to attain high biomass ranging from 0 to 248 g l-1 (31.8 6.56 g l-1). All nutrients displayed positive linear gradients from the mouth to the tidal limit, showed significant (p < 0.05) temporal and spatial variability, and were significantly (p < 0.05) correlated with phytoplankton biomass. Phytoplankton blooms (> 10 000 cells ml-1) of several different groups were recorded from the middle reaches of the estuary to the tidal limit. Diatoms were the dominant group during increased freshwater inflow (at mean daily flow rate of 2.14 m3 s-1) and low DIP levels, whereas flagellates were generally the dominant group during reduced flow and under higher nutrient levels. Although the different tidal stages had no effect on phytoplankton biomass per se, it did support co-existance between phytoplankton groups. This was noted during the spring ebb tide in September 2012 (i.e. flagellates, diatoms and dinoflagellate) and in February 2013 (i.e. dinoflagellates, diatoms and chlorophytes). Phytoplankton blooms have become persistent in the middle to upper reaches of the estuary where chlorophyll-a was > 20 µg l-1 and cell density exceeded 10 000 cells ml-1; a situation not reported in previous studies. The Motherwell Canal was and still is the main source of nitrogen (generally in the form of ammonium) to the estuary, whereas the Swartkops River is still the primary source of phosphorus to the estuary. Since the stormwater canal services the large residential area of Motherwell where leaks in the sewer system, the dumping of night soil buckets, and faulty pumps are often reported, polluted discharges from the Motherwell Canal can enter the canal at any given point. In contrast to the canal, DIP loading from the Swartkops River to the estuary generally occurred under conditions of low flow, whereas nitrogen showed no apparent relationship. Faecal bacteria originating from the Motherwell Canal had the most profound effect on the bacteriological status in the middle reaches of the estuary, whereas the Swartkops River had an intermediate effect due to bacteria die-offs occurring between the point of release from the WWTW to the riverine reaches and the tidal limit of the estuary. Nevertheless, Escherichia coli and enterococci levels are still high, especially in the summer months rendering the estuary unsafe for recreation during this season. Historical data on trace metals in the water column were limited and thus observations from the present study could not be concluded with much confidence. However, preliminary data suggest that levels of copper, zinc, iron and cadmium have increased by at least 90% in the estuary, at the tidal limit of the estuary and in the Markman and Motherwell canals. High inputs of nutrients, trace metals and faecal bacteria to the estuary from land-use activities indicate the necessity for remedial actions with the main objective being to conserve and protect the estuary’s recreational, ecological and economic functions.

Macrozoobenthic community structure and composition was investigated along a subtidal-intertidal gradient in the Mngazana Estuary. Six transects were sampled between the spring high water mark (HWST) and the bottom of the river channel in the lower estuary. Fifteen replicate samples were collected along each transect using a Van Veen type grab (211 cm2 bite) during each of three sampling sessions. Samples were sieved through a 500 μm mesh bag and the invertebrates stored in bottles for further analysis in the laboratory. Additional grab samples were collected for sediment particle size analysis and organic matter. Physical variables measured at each transect included: salinity, temperature, dissolved oxygen, depth, pH, percentage mud, organic content and turbidity. Sediment compactness was measured at all intertidal transects and additional sediment samples were collected at mid shore and high shore transects for percentage water content analysis. A total of 104 species were recorded along the intertidal-subtidal gradient in the sampling area. Species richness was higher in the subtidal zone compared to the intertidal zone and polychaetes numerically dominated the macrozoobenthic community at most transects, during all three sessions. At high shore transects the community was characterised by having fewer species, consisting mostly of brachyurans, polychaetes and gastropods. Shannon diversity index (H’) was generally higher for subtidal transects (x¯ = 2.3; range: 2.8 to 1) than for intertidal transects (x¯ = 1.4; range: 2.2 to 0.6) indicating that the distribution of individuals among species in the intertidal zone experienced greater variability. Results for Hill’s numbers followed the same trend as Shannon diversity with subtidal communities mostly consisting of abundant species followed by very abundant species. Intertidal communities generally exhibited lower numbers of abundant and very abundant species. Sedimentary characteristics played a major role in structuring benthic communities in comparison to other physico-chemical variables. Organic content and mud content of the substrate were identified as important factors influencing community patterns observed along the subtidal-intertidal gradient. In addition, sediment compactness and water content of the substrate was found to influence intertidal community structure. Subtidal community structure possibly had a greater dependence on seasonal variations in abiotic and/or biotic factors. Cluster dendrograms used in conjunction with MDS ordination mapping revealed that macrozoobenthic communities were generally distinct between high shore intertidal transects iii and subtidal transects. Most species exhibited a broad spatial distribution along the subtidal-intertidal gradient with mid and high shore transects being the exception. Most species also exhibited marked shifts in abundance and this was especially noticeable at the transition between the subtidal and intertidal zone. Two polychaete species, Prionospio sexoculata and Capitella capitata, were very abundant species and featured amongst the most numerically dominant species collected during each sampling session.