South Africa is an arid country and its growing population is putting freshwater resources under increasing pressure. Natural salinization of freshwater systems is being exacerbated by anthropogenic influences. The National Water Act (No. 36 of 1998) stipulates the need for an ecological Reserve, that quantity and quality of freshwater needed to protect freshwater ecosystems while allowing sustainable use of freshwater resources. Water guidelines do exist in the form of the South African Water Quality Guidelines (DWAF, 1996) and more recently, Jooste and Rossouw (2002) compiled benchmark values for water quality variables marking the boundaries between ecological health classes in the 4-category classification system. Predominantly international toxicity data were used to compile the guidelines and the benchmark values. In addition, there is a paucity of chronic toxicity data nationally and internationally. This thesis showed that it is statistically possible to derive protective chronic endpoints for salinity from acute toxicity data through extrapolation. The Acute to Chronic Ratio (ACR), Two-Step Linear Regression (LRA) and Multi-Factor Probit Analysis (MPA) extrapolation methods were investigated to derive chronic toxicity data from acute toxicity data. The authors of LRA and MPA recommend associating a time independent LCx value in the range of LC₀¸₀₁ to LC₁₀ with a Predicted No Effect Concentration (PNOEC). In addition to published methods, this thesis studied the possibility of equating a time independent LC₅₀ value and subjected to a safety factor of 5 (LRA LC₅₀/5), to the PNOEC. Extrapolated chronic toxicity data where the toxicants are NaCl and Na₂SO₄ were derived for indigenous South African macroinvertebrates. NaCl and Na₂SO₄ are salts associated with salinisation in South Africa. In addition, a chronic salinity toxicity test protocol for an indigenous South African aquatic macroinvertebrate was designed and chronic toxicity test were performed using NaCl and Na₂SO₄ as toxicants. The experimental chronic toxicity data produced were used to validate results from the acute to chronic extrapolation methods. Extrapolated chronic toxicity data were inputted into Species Sensitivity Distribution curves, and concentrations that were predicted to protect 95 % of species (PC95) were compared to the sub-lethality benchmarks proposed by Jooste and Rossouw (2002) for NaCl and Na₂SO₄. This study concluded that the LRA LC₅₀/5 extrapolation method is the most protective and accurate and proposed that LRA replace the ACR method in future guideline development for inorganic salts.

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.

Potentially damaging submerged invasive freshwater macrophytes have been identified in South African freshwater systems, but have received less attention than their floating counterparts. To ascertain the changes and effects that these species may have on macrophyte ecology, an understanding of the drivers of macrophyte assemblages is essential. The aims of this thesis were to investigate select abiotic and biotic factors driving introduction, establishment and spread of submerged macrophytes in South Africa. Surveys on the status of submerged plant species in South Africa were conducted to find out the distribution and diversity of the species present, imported to, and traded in South Africa. Numerous submerged indigenous and invasive macrophyte locality records were collected during field surveys, of which many were first time records. Pet stores and aquarist trading activities were identified as potential vectors for the spread of submerged macrophytes through online surveys and personal interviews. These results highlighted the potential these species have for continuing to enter, and spread within South African water bodies. Maximum Entropy (MAXENT) is a general-purpose method used to predict or infer distributions from incomplete information, and was used here to predict areas suitable for the establishment of five of these invasive macrophytes. Many systems throughout South Africa, particularly those in the subtropical coastal regions, were found to be climatically suitable for the establishment of Elodea canadensis Michx., Egeria densa Planch., Hydrilla verticillata (L.f.) Royle (all Hydrocharitaceae), Myriophyllum spicatum L. (Haloragaceae), and Cabomba caroliniana Gray (Cabombaceae). Despite the high probability of invasion, facilitated by vectors and suitable climate, South Africa’s rich indigenous submerged aquatic flora may be preventing the establishment of these submerged invasive species. Studies on the competitive interactions between a common indigenous submerged macrophytes, Lagarosiphon major (Roxb.) (Hydrocharitaceae) and M.spicatum, an invasive native to Eurasia, were conducted to ascertain which conditions influence competitive superiority. High sediment nutrient conditions significantly increased the growth rate and competitive ability of both species, while clay sediments significantly increased the competitive ability of L. major over M. spicatum, but sandy sediments improved the competitive ability of M. spicatum. These results highlighted the dynamic changes in competition between submerged species driven by abiotic factors, but did not take into consideration the effect that herbivory, a biotic factor, could have on competition between the two species. The effect of herbivory by phytophagous insects of submerged plant species has been regarded as negligible. To find out what this effect is, multiple field surveys were undertaken throughout South Africa to find natural enemies of indigenous Lagarosiphon species with the aim of identifying such species, and quantifying their influence on plant growth dynamics. Several new phytophagous species were recorded for the first time. An ephydrid fly, Hydrellia lagarosiphon Deeming (Diptera: Ephydridae) was ascertained to be the most ubiquitous and abundant species associated with L. major in South Africa. The influence of herbivory by this fly on the competitive ability of L. major in the presence of M. spicatum was investigated using an inverse linear model, which showed that herbivory by H. lagarosiphon reduced the competitive ability of L. major by approximately five times in favour of M. spicatum. This study served to highlight the importance of herbivory as a driver of submerged aquatic plant dynamics. Current ecological theory emphasises the importance of investigating beyond plant-herbivore interactions, by including multitrophic interactions in community dynamics. Therefore, the potential of parasitism by a parasitoid wasp, Chaenusa luteostigma sp. n. Achterberg (Hymenoptera: Braconidae: Alysiinae) on H. lagarosiphon to shift the competitive interactions between the two plant species was also examined. The addition of the parasitoid reduced the effect of herbivory by the fly on L. major by half, thereby shifting the competitive balance in favour of L. major over M. spicatum. This study provides valuable insight into a selection of drivers of submerged macrophyte assemblages of South Africa. It highlights the precarious position of South African freshwater systems with regard to the potential invasion by damaging submerged invasive species. It also provides interesting insights into the effect of competition, herbivory and parasitism on the establishment and spread of species within submerged freshwater systems. Understanding the different influences could assist managers and policy makers to make validated decisions ensuring the integrity of South African freshwater systems.

The nutrient dynamics in two contrasting estuaries and in the adjacent nearshore environment along the south-east coast of South Africa was investigated seasonally. Due to an inter-basin transfer of water from the Gariep Dam to the Great Fish River, the Great Fish estuary is a fresh water dominated, terrestrially driven system with an annual fresh water inflow of 250 – 650 x 10⁶ m³ per year. In contrast, the Kariega estuary is a fresh water deprived, marine dominated system with a fresh water inflow estimated at 2.5 – 35 x 10⁶ m³per year. The reduced fresh water inflow into the estuary is attributed to regular impoundments along the Kariega River. Water samples were collected from surface and subsurface layers along the length of the estuaries as well as from a series of transects occupied in the nearshore environment. Samples were analysed for nitrate, nitrite, ammonium, phosphate and silicate. Temperature and salinity were recorded at each station. A Land-Ocean Interactions in the Coastal Zone (LOICZ) budget was constructed for each estuary to describe the role of ecosystem-level metabolism as either a sink or a source of phosphorus, nitrogen and carbon. Seasonal variation in physico-chemical properties and nutrient concentrations in the Kariega estuary was minimal due to constant low inflow, while in the Great Fish estuary, concentrations varied in response to changes in flow rate. Nutrient concentrations were consistently higher in the Great Fish estuary than in the Kariega estuary, largely reflecting differences in fresh water inflow. During periods of high flow (32.92 m³.s⁻¹in the Great Fish River) dissolved inorganic nitrogen (DIN) concentrations in the Great Fish estuary were an order of magnitude higher than those recorded in the Kariega estuary. Results of the LOICZ budgeting procedures revealed that in spite of the contrasting hydrodynamic features, the estuaries behave in largely the same manner – both predominantly sources of nutrients with heterotrophic processes dominating over autotrophic actions and both were net denitrifyers during all surveys. This was, however, due to different sets of processes operating in the two estuaries, namely low nutrient concentrations resulting in microbial activity in the Kariega estuary, and riverine influx of nutrients and phytoplankton combined with a short residence time of the water in the Great Fish estuary. In the marine nearshore environment, higher nutrient concentrations were recorded adjacent to the Great Fish estuary than offshore of the Kariega estuary. This was due to a surface plume of less saline water leaving the Great Fish estuary, which acted as an ‘outweller’ of nutrients. Offshore of the Kariega estuary, on the other hand, the nutrient concentrations were characteristic of marine waters due to a lack of fresh water outflow from the estuary. Nutrient concentrations in the marine environment adjacent to the Kariega estuary were, at times, higher than those recorded within the estuary. This observation supports previous statements which suggest that the Kariega estuary is not an ‘outweller’ of dissolved nutrients and particulate material, but rather an extension of the marine environment.

In common with other natural systems, aquatic ecosystems provide a wealth of economically valuable services and long-term benefits to society. However, growing human populations, coupled with increased aspirations for improved quality of life, have lead to intense pressure on the world's finite freshwater resources. Frequently, particularly in developing countries, there are both perceived and genuine incompatibilities between ecological and societal needs for freshwater. Environmental Flow Assessment (EFA) is essentially a tool for water resources management and its ultimate goal should be the integration of ecological and societal systems. While other ecological components (i.e. biological and geomorphological) are equally important to EFA, this thesis investigates the role of the hydrological cycle and the hydrological regime in providing the ecosystem goods and services upon which society depends. Ecological and societal systems operate at different temporal, spatial and organisational scales and hydronomic zoning or sub-zoning is proposed as an appropriate water resources management technique for matching these different scales. A major component of this thesis is a review of the South African water resources management framework and, in particular, the role of the Reserve (comprising a basic human right to survival water as well as an ecological right of the aquatic resource to maintain ecological functioning) in facilitating ecologically sustainable water resources management. South African water resources management is in the early stages of water allocation reform and the Department of Water Affairs and Forestry has stated that "the water allocation process must allow for the sustainable use of water resources and must promote the efficient and non-wasteful use of water". Thus, new ways of approaching the compromise between ecological and societal needs for freshwater water are required. This thesis argues that this requires that the focus of freshwater ecosystems be extended beyond the aquatic resource, so that societal activities on the catchment are linked to the protection of instream flows. Streamflow variability plays a major role in structuring the habitat templates that sustain aquatic and riparian ecological functioning and has been associated with increased biodiversity. Biodiversity and societal well-being are interlinked. However, there is a need in EFA for knowledge of the most influential components of the streamflow regime in order that stakeholders may anticipate any change in ecosystem goods and services as a result of their disruption to the hydrological cycle. The identification of high information hydrological indicators for characterising highly variable streamflow regimes is useful to water resources management, particularly where thresholds of streamflow regime characteristics have ecological relevance. Several researchers have revisited the choice of hydrological indices in order to ascertain whether some indices explain more of the hydrological variability in different aspects of streamflow regimes than others. However, most of the research relating to hydrological indices has focused primarily on regions with temperate climates. In this thesis multivariate analysis is applied to a relatively large dataset of readily computed ecologically relevant hydrological indices (including the Indicators of Hydrological Alteration and the South African Desktop Reserve Model indices) extracted from long-term records of daily flows at 83 sites across South Africa. Principal Component Analysis is applied in order to highlight general patterns of intercorrelation, or redundancy, among the indices and to identify a minimum subset of hydrological indices which explain the majority of the variation among the indices of different components of the streamflow regimes found in South Africa. The results indicate the value of including several of the IHA indices in EFAs for South African rivers. Statistical analysis is meaningful only when calculated for a sufficiently long hydrological record, and in this thesis the length of record necessary to obtain consistent hydrological indices, with minimal influence of climatic variation, is investigated. The results provide a guide to the length of record required for analysis of the high information hydrological indices representing the main components of the streamflow regime, for different streamflow types. An ecosystem-based approach which recognises the hydrological connectivity of the catchment landscape in linking aquatic and terrestrial systems is proposed as a framework for ecologically sustainable water resources management. While this framework is intended to be generic, its potential for application in the South African Water Allocation Reform is illustrated with a case study for the Mkomazi Catchment in KwaZulu-Natal. Hydronomic sub-zoning, based on the way in which societal activities disrupt the natural hydrological processes, both off-stream and instream, is applied to assess the incompatibilities between societal and ecological freshwater needs. Reference hydrological, or pre-development, conditions in the Mkomazi Catchment are simulated using the ACRU agrohydrological model. Management targets, based on the statistical analysis of pre-development streamflow regimes, are defined to assess the degree of hydrological alteration in the high information hydrological indices of the Mkomazi Catchment as a result of different societal activities. Hydrological alteration from predevelopment conditions is assessed using the Range of Variability Approach. The results indicate that the proposed framework is useful to the formulation of stakeholder-based catchment management plans. Applying hydrological records (either observed or simulated) as an ecological resource is highly appropriate for assessing the variability that ecosystems need to maintain the biodiversity, ecological functioning and resilience that people and society desire. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.

Although the use of pesticides is necessary to meet the socio-economic needs of many developing countries, especially in Africa, side effects of these bio-active chemicals have contributed to contaminating aquatic and terrestrial ecosystems. Environmental water quality degradation by pesticides interferes with ecosystem health and poses numerous risks to aquatic life. In South Africa, glyphosate-based herbicides are frequently used to control weeds and invading alien plants, but ultimately end up in freshwater ecosystems. However, there are no South African-based environmental water quality management strategies to regulate these bio-active chemicals. Therefore, this study sought to provide a sound scientific background for the environmental water quality management of glyphosate-based herbicides in South Africa, by conducting both laboratory and field investigations. In the laboratory investigations, aquatic ecotoxicological methods were used to evaluate responses of the freshwater aquatic shrimp Caridina nilotica exposed to Roundup® at different biological system scales, and the responses of multiple South African aquatic species exposed to Roundup® through species sensitivity distribution (SSD). In the field investigations, the effect of Kilo Max WSG on the physicochemical and biological conditions of three selected sites in the Swartkops River before and after a spray episode by Working for Water were evaluated through biomonitoring, using the South African Scoring System version 5 (SASS5) as a sampling protocol. Both Roundup® and Kilo Max WSG are glyphosate-based herbicides. All the data were subjected to relevant statistical analyses. Findings of this study revealed that Roundup® elicited responses at different biological system scales in C. nilotica, while SSD estimates were used to derive proposed water quality guidelines for glyphosate-based herbicides in South Africa. The biomonitoring revealed that using glyphosate-based herbicides to control water hyacinth within the Swartkops River had a negligible impact on the physicochemical and biological conditions. Based on these findings, a conceptual framework that can be used for the integrated environmental water quality management of glyphosate-based herbicides in South Africa was developed as part of integrated water resource management (IWRM). The combined data sets contribute to a sound scientific basis for the environmental water quality management of glyphosate-based herbicides in South Africa.

Freshwater resources are increasingly subject to pollution because of escalating human population growth, accompanied by urbanisation, industrialisation, and the increased demand for food. Consequently, freshwater quality, and aquatic ecosystem structure and function have been severely impaired. The Swartkops River, which drains an urbanised and industrialised catchment in the Eastern Cape of South Africa, is no exception. An integrated environmental water quality (EWQ) approach is needed to measure the impacts of deteriorating water quality on its aquatic ecosystem structure and function to sustain these vital ecosystem-attributes. In this study, an integrated EWQ approach, which included i) analysis of water physico-chemical variables; ii) macroinvertebrate-based family-level taxonomic- and traits-based community analysis; iii) Chironomidae species-level taxonomic- and traits-based community analysis; iv) Chironomidae deformity-based sub-lethal analysis; and v) experimental investigation of long-term wastewater effluent effects, using model stream ecosystems, were applied to investigate environmental water quality in the Swartkops River. One upstream reference site and three downstream sites in the Swartkops River were monitored over a period of three years (August 2009 – September 2012). The family-level taxonomic community responses based on the South African Scoring System version 5 (SASS5) and a newly developed Swartkops multimetric index indicated very poor river health conditions for the three downstream sites, compared with the good condition of the upstream site. The Chironomidae species-level responses in the three downstream sites provided evidence of differences in biotic impairments, which were not evident with the family-level taxonomic data at these sites, thus highlighting the importance of species identification in freshwater biomonitoring. The family-level traits-based approach (TBA) showed that macroinvertebrates with gills and lungs were more abundant at the upstream site, decreasing markedly at the downstream sites. The relative abundance of macroinvertebrates relying on aerial and tegument respiration increased at the downstream sites compared with the upstream sites. The results of the family-level TBA highlighted the inextricable link between the traits-based approach (TBA) and taxonomic identification, clearly showing that the TBA is additional to, and not an alternative to, taxonomic recognition because important traits, e.g. reproductive cannot be used at a coarse taxonomic identification. A novel chironomid species traits-based functional strategies approach developed in this study, based on species combining similar sets of traits, proved sensitive in diagnosing the main abiotic water physico-chemical stressors. The functional traits responded predictably to deteriorating water quality and provided an adaptive and mechanistic basis for interpreting chironomid species occurrences at the four sampling sites, providing insight into why certain chironomid species occurred at one site but not at the other. Chironomid deformities provided evidence of sub-lethal in-stream biological response to deteriorating water quality. A newly developed deformity-based extended toxic score index proved sensitive, enabling the discrimination of the sampling sites, indicating that a biomonitoring tool based on sub-lethal effects could be used to assess the effects of deteriorating water quality before it reached lethal levels. Empirical evidence based on the taxonomic, traits and sub-lethal responses suggested that the changes in macroinvertebrate community structure were caused chiefly by the discharge of wastewater effluents into the river. This was supported by the model-stream ecosystem results indicating significant effects of effluents on the macroinvertebrate community structure, similar to the observed in-stream responses. The model stream results indicated that improved physico-chemical effluent quality compliance after 50% effluent dilution did not significantly reduce the effects of the effluent on the macroinvertebrate communities, showing that ecologically-based methods rather than physico-chemical measures alone are necessary to assess effluent quality. Finally, the results of the multi-criteria approach were integrated to propose tools to manage environmental water quality in the Swartkops River, and the benefits of the study were highlighted in the context of biomonitoring in South Africa.