Temporary rivers in dryland regions are subject to highly variable and unpredictable rainfall and flow, and are considered unstable systems relative to perennial rivers of temperate zones. Little is known of the ecology of South Africa's temporary rivers, despite their abundance. The research presented focusses on the aquatic invertebrates inhabiting intermittently-flowing rivers in the 'arid corridor' of the Eastern Cape, South Africa. The major aims of the work were: to investigate which invertebrates inhabit these rivers, how the fauna is affected by environmental variability at various spatial and temporal scales, whether or not a characteristic fauna can be associated with these rivers or the hydrological phases which characterise them, and to establish to what extent faunal overlap occurs between different temporary rivers and between natural and modified temporary and perennial rivers. Research results indicate that the fauna of the Eastern Cape temporary rivers shows little structure at the scales of investigation, and that communities are generally non-equilibrial in character. The major forces shaping the biota are considered to be physical rather than biological, and the most important of these are: present and antecedent hydrological conditions and their duration; time of year; and biotope character, extent and heterogeneity. Three groups of fauna were identified as inhabitants of the temporary rivers: 'residents', 'facultative taxa' and 'opportunist colonists'. Taxa were tentatively allocated to these groups. Faunal resemblance was fairly high in Eastern Cape temporary rivers at the level of family, but not at more detailed taxonomic levels. A comparison between faunas of temporary and perennial rivers in different regions of South Africa illustrated the influence of geographical location on diversity. Within regions, however, there was no indication that perennial rivers were more diverse than intermittent rivers. The relatively high diversities in temporary rivers in this study are attributed at least in part to the heterogeneity in surface water conditions over time. A conceptual framework envisioning a continuum between perennial and temporary rivers is proposed as a basis for ongoing research into these rivers. A supporting terminology for the range of river flow types in South Africa is presented.

Thesis (PhDEng)--University of Stellenbosch, 2002. / ENGLISH ABSTRACT: The interaction between moving water and the physical attributes of a river, as displayed by the channel morphology, determines the availability of physical habitat for aquatic species and thus also the condition of the ecosystem. As such, the environmental flow assessment process requires knowledge on how changes in the flow regime will affect both the morphological and hydraulic conditions within a river channel. With the increasing development of water-related infrastructure in mountain regions, knowledge of the morphological and hydraulic characteristics of rivers in the upper catchment areas is very important. Cobble and boulder bed rivers in the Western Cape are typical examples. They are characterized by steep gradients, great variability in sediment size and relatively low flow depths. The bed configuration contains a series of pools, steps, rapids, riffles and plane beds, while energy losses are high as a result of turbulence and hydraulic jumps. Due to their wideranging morphological and associated hydraulic attributes, the physical habitats within these rivers are extremely diverse, both on a spatial and temporal scale. This study addresses the interaction between moving water and the physical attributes of cobble and boulder bed rivers. Empirical, semi-empirical and theoretically based models are developed which define the hydraulic and morphological related characteristics of environmental flow components in cobble and boulder bed rivers. They cover macro scale channel deformation, the scouring of sand from the interstitial spaces between the cobbles as well as velocity-depth relationships, which prove to be key components in the assessment of environmental flow requirements in cobble and boulder bed rivers. / AFRIKAANSE OPSOMMING: Die wisselwerking tussen die vloeiende water en die fisiese eienskappe van 'n rivier, soos beskryf deur die morfologie, bepaal die beskikbaarheid van habitat vir akwatiese spesies en gevolglik ook die welstand van die ekosisteem. Kennis omtrent die impak van 'n veranderde vloei regime op beide die morfologiese en die hidrouliese toestande in 'n rivierloop is dus nodig vir die bepaling van omgewingsvloeibehoeftes. Met die toenemende ontwikkeling van water-verwante infrastruktuur in bergagtige gebiede is 'n grondige kennis van die morfologiese en hidrouliese eienskappe van riviere in hierdie bo-opvanggebiede gebiededend noodsaaklik. Spoelklip riviere in die Wes-Kaap is tipiese voorbeelde van sulke riviere. Hierdie riviere word gekenmerk deur steil hellings, 'n wye verskeidenheid sedimentgroottes, relatiewe lae vloeidieptes en hoë energieverliese as gevolg van turbulensie. Verder bevat die ri vierbed afwisselend poele en stroomversnellings en gevolglik word 'n wye verskeidenheid habitat tipes in hierdie riviere aangetref. Hierdie studie fokus op die interaksie tussen bewegende water en die fisiese eienskappe van spoelklip riviere. Met behulp van empiriese, semi-empiriese en teoretiese modelle word die morfologiese en hidrouliese eienskappe van omgewingsvloeibehoeftes in spoelklip riviere aangespreek. Dit sluit makroskaal kanaal vervorming, die uitskuur van sand tusen die spoelklippe asook die verwantskap tussen vloeisnelheid en vloeidiepte in. Hierdie aspekte kan beskou word as van die sleutel elemente vir die bepaling van omgewingsvloeibehoeftes in spoelklip riviere.

Thesis (MScEng (Civil Engineering))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: In this research a Real-Time hydrodynamic optimisation model of the Orange-Fish-Sundays River (OFS) system which uses real-time data in order to forecast release hydrographs, is evaluated. The OFS system stretches over three catchment areas in the Eastern Cape namely Great Fish, Little Fish and Sundays Rivers. The OFS supplies water from the Orange River through a 800 km system of canals, tunnels, dams and rivers to registered water users in this area. In order to cope with increasing pressures on water saving, water demand, water quality and dam safety, the Department of Water Affairs implemented this Orange Fish Sundays-Real Time (OFS-RT) system to calculate the optimal water flow, by running customised Danish Hydraulic Institute (DHI) MIKE11 software. The system utilizes an optimisation module that evaluates the simulated outcome at seven water release structures (dams, weirs and tunnels). Then during the optimisation process performs more adjustments to reach the objectives of the system to obtain the forecast release hydrographs. This OFS-RT model aims at target based objectives, using: (i) Hydras real-time field data of dam water levels, river flows and water quality from the area sent to the control office main computer at four hourly intervals via SMS and (ii) abstractors weekly water requests. This system takes irrigation and domestic demand into account as well as water quality, evaporation, rainfall, dam levels, dam safety, instream flow requirements and tributary flow. In order to manage the water flows through the OFS system the OFS-RT model forecasts the release hydrographs and uploads the predictions to a website to smooth operational procedures. The target outcomes were tested and evaluated during this research and it was found that the OFS- RT model succeeded in delivering release forecasts for the seven control structures to manage the OFS system. This research proved that management of river systems by using a real-time hydrodynamic model with optimisation is a useful tool for the optimal utilisation of water resources. / AFRIKAANSE OPSOMMING: Die doel van hierdie navoring is die evaluering van „n intydse hidrodinamiese optimiseringsmodel van die Oranje-Vis-Sondagsrivier (OVS) stelsel wat intydse data ontvang en loslatings hidrograwe verskaf. Die OVS stelsel strek oor drie opvangsgebiede in die Oos-Kaap: naamlik die Groot Vis-, Klein Vis- en Sondagsriviere en voorsien water vanuit die Oranjerivier deur „n 800 km stelsel van kanale, tonnels, damme en riviere, aan geregistreerde waterverbruikers in die gebied. Ten einde te voldoen aan die eise van waterbesparings, stygende vraag na water, die verskaffing van goeie water gehalte en damveiligheid, het die Departement van Waterwese „n intydse rekenaar model (OVS-IT) geïmplimenteer om die optimale watervloei deur middel van die aangepaste MIKE11 sagteware van die Danish Hydraulic Institute (DHI) te bereken. Hierdie stelsel maak gebruik van „n optimisering module wat die gesimuleerde uitkomste van verstellings aan sewe waterloslatingstrukture evalueer. Met optimisering word die verlangde hidrograaf deur verder aanpassings verkry. Data wat nodig is om die OVS-IT model se doel te bereik is: (i) Hydras intydse velddata van damwatervlakke, riviervloeie en water gehalte van die gebied ontvang deur die beheerkantoor se hoofrekenaar via SMS elke vier ure, en (ii) water verbruikers se weeklikse wateraanvrae Die stelsel neem die besproeiing en huishoudelike aanvraag in ag, sowel as soutgehalte, verdamping, reënval, damvlakke, dam veiligheid, stroom vloei vereistes en sytak byvloei. Die OVS se watervloei word beheer deur voorspelde loslatings hidrograwe, opgesom op „n webwerf wat die uitvoer prosedures aandui. Die intydse hidrodinamiese model met optimisering het volgens hierdie navorsing daarin geslaag om vir die beheer van die OVS stelsel, die loslatings van sewe beheerstrukture akkuraat te voorspel en bevind dat die model „n waardevolle instrument is vir die optimale bestuur van waterhulpbronne.

MSc., Faculty of Science, University of the Witwatersrand, 2011 / Sodic soils are salt-affected soils which are high in sodium in relation to magnesium and calcium. Commonly called sodic sites in the Kruger National Park (KNP), these patches exhibit unique functional characteristics due to the high levels of sodium which cause surface crusting, cracking and the dispersion of clay particles. The aim of this study is to use satellite imagery to map sodic sites in the KNP at different spatial and spectral scales, giving the best option for a repeatable, semi-automated classification. The resultant map of sodic sites for the KNP will be used as a management tool and for future research projects. A field test for sodicity was necessary to collect sufficient ground truth samples for robust accuracy assessment of the image classification. Sodic soils are identified by measuring EC, pH and SAR which are highly variable within site and between testing methods, and therefore not useful for rapid ground truth classification of sodic soils in the field. The sodium level at which clay particle dispersion takes place varies between soils, but is measurable in the field using the Emerson dispersion test. Laboratory tested sodic soil sites from previous research re-tested in this study showed positive results for dispersion of clay particles in water. The physical properties of sodic sites described in the literature and observed in the field were applied to classify sodic sites in the KNP in the field using a decision tree, together with results from the dispersion test and the observed presence of the grass species Sporobolus iocladus. Landsat 7 and SPOT 5 imagery cover the whole park, with ASTER, CAO hyperspectral, LiDAR and black and white orthophotos available for selected areas. The topography elements of crest and footslope were derived from the STRM 90m digital elevation model (DEM). Image preprocessing to top of atmosphere reflectance was performed where necessary and visual enhancement techniques and transformations were applied to derive the normalised difference vegetation index (NDVI) and other indices. Spectral signatures were checked against spectral signature libraries, and the class separation was tested using the cluster analysis of spectral signatures. MODIS NDVI averages placed the imagery in phenological context. Object-based image analysis using eCognition was applied to classify the sodic sites of the Shingwedzi and Ripape River catchments. The input imagery was segmented into ecologically meaningful patches and classification accuracy was assessed using the field samples collected using the decision tree to identify four classes: sodic sites (bare and woody), river sand, riverine vegetation and savanna areas. Comparison of the accuracy assessments for the Shingwedzi study site showed that the Landsat 7 and SPOT 5 classification algorithms gave an overall kappa index accuracy of 89% and 78% respectively, and a sodic site kappa index of 90% and 89%. Validation results using the ground truth samples gave an overall kappa index accuracy of 61% for Landsat 7 and 52% for SPOT 5, with a sodic site kappa index of 49% and 39% respectively. The classification algorithms were applied to the Ripape study site for Landsat 7 and SPOT 5 with repeatable results for the SPOT 5 imagery of 88% overall kappa index and 81-93% kappa index for sodic sites using similar seasonal imagery in the wet to early dry season. The Landsat 7 classification algorithm was applied to the entire KNP based on the repeatability results of 56% overall kappa index and 60% sodic site kappa index for the Ripape site. The quest for a repeatable algorithm to classify sodic sites from satellite imagery has been met by the SPOT 5 imagery using scenes acquired at similar seasonal stages. The late wet season or early dry season imagery was used to apply the classification algorithm with the best success. Changes in size or shape of sodic sites over time requires very high resolution imagery and further studies to understand where the edge of sodic sites are detected from imagery, and how the phenology of the vegetation growing on these sites affects detecting any change in size of the sodic site.

Thesis submitted in fulfilment of the requirements for the degree Master of Technology: Biomedical Technology in the Faculty of Health and Wellness Sciences at the Cape Peninsula University of Technology, 2012 / In many developed countries worldwide the provision of safe, clean water is an expected commodity. In South Africa however, as in most developing countries, the access and supply of water safe for human consumption is challenged or complicated by pollution and more recently water availability. Point-source pollutants in surface- and groundwater are normally the most concentrated closest to the pollutant source (such as the end of a pipe or an underground injection system). Examples of point-source pollution are commercial and industrial businesses, that often discharge waste such as solvents and heavy metals from their operations. In contrast, non-point-source pollution occurs due to runoff moving across or through the ground and absorbing and accumulating pollutants which eventually end up in streams, rivers and dams. The lack of waste removal and adequate sanitation facilities results in the disposal of faecal matter and sewage into storm water drains which flow directly into the river systems contributing to the incidence of diseases such as gastroenteritis, diarrhoea and chronic lung ailments, caused by waterborne pathogenic bacteria, viruses and fungi. Routine water quality analysis however, does not include monitoring for viral contaminants, as this process is hampered by the lack of simple, reliable, time- and cost-effective testing methods to concentrate and detect viral pathogens. The primary aim of this study was thus to establish and optimise routine monitoring techniques for the detection of rota-, adeno- and enteroviruses in the Berg- and Plankenburg Rivers, Western Cape. Initially, various concentration and extraction methods were compared for the optimum recovery of viruses from spiked water samples. One hundred milliliter water samples were spiked with one milliliter rotavirus and two milliliters adenovirus control virions (Coris Bioconcept, Gembloux, Belgium). Optimisation testing of enterovirus was however, not completed due to the unavailability of a positive control. Four viral concentration techniques, namely the Silicon dioxide (SiO2) method, positively charged, negatively charged and the mixed-ester filters, were compared. Various nucleic acid extraction methods were also employed to establish which method would provide optimum yields for both DNA and RNA nucleic acids. The extraction techniques included the TRIzol method (Invitrogen, California, USA) for RNA extraction, the Roche High Pure PCR Template Preparation kit (Roche, Mannheim, Germany) for DNA extraction, and the QIAamp Ultrasens Virus kit (Qiagen GmbH, Hilden, Germany) for simultaneous RNA and DNA extraction. The use of virus specific primers within the PCR technique was also optimised. In addition, gene specific primers and oligo(dT)15 primers were tested and compared to establish which primers would yield the best results since gene specific primers are said to be more sensitive than oligo(dT)15 primers (van Pelt-Verkuil et al., 2008) when synthesising cDNA (rotavirus). The SiO2 concentration method yielded variable results when it was used with the various nucleic acid extraction techniques in this study, since positive PCR results were obtained when used in combination III with some techniques, while negative results were obtained with others. Similarly, variable results were also obtained when negatively charged filters were used to concentrate virus particles, and when this method was used in conjunction with various virus nucleic acid extraction techniques to identify different viruses by RT-PCR and PCR. Results for the non-charged mixed-ester filter were comparable to the positively charged filters when used in conjunction with the various nucleic acid extraction techniques in this study. Both these techniques yielded the highest viral particle concentration from the spiked water samples. Pilot study results indicated the presence of rotavirus and adenovirus detected by RT-PCR and PCR respectively, when filtering through the positively charged filter. The positively charged filter/QIAamp UltraSens virus kit combination was found to be the optimum combination when analysing the spiked water results and was then employed for the concentration of virus particles in the river water samples collected from the Plankenburg- and Berg River systems throughout the study period. The expected PCR product of 346 bp for rotavirus was absent in all 72 river water samples analysed for both river systems. In contrast to the PCR results obtained for rotavirus, the expected product of 261 bp for adenovirus was detected in 22 (30.5%) samples collected throughout the study period. Fifteen of the 22 adenovirus positive samples were found in the Plankenburg River (distributed over all sites), while seven of the 22 adenovirus positive samples were found in the Berg River (all sites). A nested PCR was used to detect enterovirus in the river water samples collected from both river systems throughout the study period. In the first round of the enterovirus PCR 15 river water samples (at various sites for both river systems) yielded a faint 513 bp product. Further amplification by nested PCR then yielded 13 (18.1%) positive nested PCR products of 297 bp. The incidence of adenovirus and enterovirus in river waters reported in the current study and the Van Heerden et al. (2003) investigation motivates for similar studies to be conducted in drinking water, dam water used for recreational purposes as well as rainwater, which is gaining popularity as a sustainable water source.

Thesis (MTech (Biomedical Technology))--Cape Peninsula University of Technology, 2012. / In many developed countries worldwide the provision of safe, clean water is an expected commodity. In South Africa however, as in most developing countries, the access and supply of water safe for human consumption is challenged or complicated by pollution and more recently water availability. Point-source pollutants in surface- and groundwater are normally the most concentrated closest to the pollutant source (such as the end of a pipe or an underground injection system). Examples of point-source pollution are commercial and industrial businesses, that often discharge waste such as solvents and heavy metals from their operations. In contrast, non-point-source pollution occurs due to runoff moving across or through the ground and absorbing and accumulating pollutants which eventually end up in streams, rivers and dams. The lack of waste removal and adequate sanitation facilities results in the disposal of faecal matter and sewage into storm water drains which flow directly into the river systems contributing to the incidence of diseases such as gastroenteritis, diarrhoea and chronic lung ailments, caused by waterborne pathogenic bacteria, viruses and fungi.

Subsistence fishing is impacting on freshwater and marine biodiversity to the extent of extinction of some fish species. These illegal subsistence fishermen have created a huge impact on marine biodiversity, irrespective of marine and riverine laws that are put in place and practiced. There have been attempt to provide subsistence fishing extension officer services to facilitate in bringing subsistence fishermen fully into the management system, in an orderly and equitable manner, by facilitating the granting of formal subsistence fishing right, providing permits via policy management and effective rules via permit applications. However the follow up process as to whether these policies and rules administered is effective or not has not been measured. This investigation attempts to identify potential fishing that should be considered as suitable for subsistence fisheries in selected highly exploitable areas. Though it cannot be confirmed from previous studies that some relevant organizations are not fully taking their responsibilities, the study will further enable exploration of options and challenges associated with future management of subsistence fisheries and provide recommendations to enable proper implementation of the policies and legislations. / Environmental Sciences / M. Env. Sc. (Agriculture and Environmental Affairs)

Thesis (MSc)--University of Stellenbosch, 2002. / ENGLISH ABSTRACT: In this study, the Fish Assemblage Integrity Index (FAll) was applied on three rivers within the southwestern Cape. This index uses fish as indicators of biological aquatic integrity and is based on indigenous species expected to be present in biological fish habitats. Fish integrity classes were calculated for each of the sites in the three rivers studied. Sites 2 and 4 within the Lourens River were rated as Class C, whereas sites 1 and 3 were rated as Class F and Class D respectively. Sites 1, 2 and 4 within the Palmiet River were rated Class F, whereas sites 3 and 5 were rated as Class E and Class D respectively. Site 1 within the Hout Bay River was rated as a Class F site, in addition to sites 2 and 3 been rated as Class A. It is however, suggested that the FAll needs to be adjusted to accommodate the general low species richness experienced in the southwestern Cape. In addition to the FAll been applied, the effects of long-term exposure to subtle water quality changes associated with human activities, specifically potential estrogenic compounds in fish from the Lourens River were also investigated. The production of the yolk precursor lipoprotein complex, vitellogenin (Vtg) produced in the liver under estrogen control was employed as biomarker for environmental estrogen exposure. Male fish from the Lourens River were studied using SDS-PAGE gel electrophoresis. Results indicated that 60% of male fish showed the presence of Vtg in their plasma. Abnormal gonad morphology in male and female fish were also assessed using standard histological procedures. Results from this study indicated no observed abnormalities in either male or female gonads. The immediate presence of endocrine disrupters with estrogen activity was investigated by screening water samples from the Lourens, Palmiet and Hout Bay Rivers for estrogen activity. Results indicated that none of the samples appeared to be cytotoxic. In addition, estrogen activity of water samples was also investigated by in vitro culturing of water samples with frog, Xenopus laevis, liver slices. Results indicated that none of the water samples from the three rivers studied indicated estrogenic activity. Although cytotoxicity and estrogen activity results were negative, the production of Vtg in male fish suggests further research regarding the presence of estrogenic substances in these rivers. / AFRIKAANSE OPSOMMING: In die huidige studie is die 'Fish Assemblage Integrity Index' (FAIl) toegepas op drie rivere in die suidwes Kaap. Hierdie indeks gebruik visse as bioindikatore van biologies akwatiese integriteit en is gebasseer op die inheemse visspesies wat verwag word in biologiese vishabitatte. Integriteitsklasse is bepaal vir elke studieterrein in die drie rivere wat ondersoek is. 'n Klas C is bepaal vir studieterreine 2 en 4 in die Lourensrivier. Klas F en Klas D is bepaal vir studieterreine 1 en 3 in die rivier onderskeidelik. 'n Klas F is bepaal vir studieterreine 1, 2 en 4 en Klas E en Klas D bepaal vir studieterreine 3 en 5 in die Palmietrivier onderskeidelik. 'n Klas F is bepaal vir studieterrein 1 in die Houtbaairivier waar 'n Klas A bepaal is vir studieterreine 2 en 3. Dit word egter voorgestel dat die FAII aangepas moet word om die algemene lae spesierykheid wat ervaar word in die suidwes Kaap te akkomodeer. Die reaksie van visse, afkomstig van die Lourensrivier, op die langtermyn blootstelling aan estrogeniese stowwe is ook bestudeer. Spesifieke reaksies van endokriene versteuring, soos vitellogeen (Vtg) produksie in manlike visse is ondersoek deur middel van SDS-PAGE gel elektroforese. Resultate toon dat in 60% van die manlike visse Vtg in die plasma teenwoordig was. 'n Ondersoek na abnormale gonade morfologie in manlike en vroulike visse van die Lourensrivier is deur standard histologiese prosedures gedoen. Resultate hiervan dui op geen sigbare abnormaliteite in die gonades nie. Die onmiddelike teenwoordigheid van endokriene versteurders is bestudeer deur die sitotoksisiteit van watermonsters afkomstig van die Lourens, Palmiet en Houtbaai riviere te bepaal. Resultate dui aan dat geen monsters sitotoksies was nie. Die estrogeenaktiwiteit van die watermonsters is ook ondersoek deur van in vitro kulture van watermonsters saam met padda, Xenopus leavis, lewersnitte gebruik te maak. Geen estrogeniese aktiwiteit is in die watermonsters gevind nie. Al is die sitotoksisiteit en estrogeenaktiwiteit resultate negatief, dui die produksie van Vtg in manlike visse op die noodsaaklikheid van verdere navorsing ten opsigte van die teenwoordigheid van estrogeniese stowwe in drie riviere.

A dissertation Submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, for the Degree of Master of Science. . / The cyclone Domoina floods of 1984 were responsible for the large scale destruction and devastation of riverine vegetation in the Umfolozi Game Reserve. This event highlighted the need to gain an understanding af the structure and dynamics of riverine vegetation and to use this knowledge to develop a management strategy directed at the future recovery and maintenance of riverine vegetation in the Umfolozi Game Reserve. (Abbreviation abstract) / Andrew Chakane 2018

This study assesses the presence of selected trace metals and pops in the Baynespruit River, Sobantu, KwaZulu-Natal. Sediments, plants and water samples were collected along the river during dry and wet season. For metal analysis, the extraction was done using acid digestion and then determined on the inductively coupled plasma atomic emission spectroscopy, for total metals in sediments, plants and water. Bio-available metals in sediments were analysed using atomic absorption spectroscopy. POPs were extracted in sediments using soxhlet extraction, which was followed up by evaporation on the rotary evaporator, sample clean up on a GPC column, further sample concentration on the rotary evaporator and later analysed on GC/MS instrument. Metals of concern in both seasons were Cu, Cr, Pb and Zn which exceeded maximum permissible limits for South African soil, Cr was just about the maximum permissible limit. The targeted POPs were not detected on any site during this work. / Environmental Sciences / M. Sc. (Environmental Science)