The National Water Act (Act 36 of 1998) provides for an ecological Reserve as the quantity (flow) and quality of water needed to protect aquatic ecosystems. While there are methods available to quantify the ecological Reserve in terms of flow, methods of linking flow to water quality are lacking. Therefore, the research presented in this thesis investigated various modelling techniques to estimate the effect of flow on water quality. The aims of the research presented in this thesis were: Aim 1: Can the relationship between flow and water quality be accurately represented by simple statistical models? Aim 2: Can relatively simple models accurately represent the relationship between flow and water quality? Aim 3: Can the effect of diffuse sources be omitted from a water quality model and still obtain realistic simulations, and if so under what conditions? Aim 4: Can models that solely use historical monitoring data, accurately represent the relationships between flow and water quality? In Chapter 3, simple Q-C regressions of flow and water quality were investigated using Department of Water Affairs (DWA) historical monitoring data. It was found that while flow versus salinity regressions gave good regression fits in many cases, the Q-C regression approach is limited. A mechanistic/statistical model that attempted to estimate the point and diffuse signatures of nutrients in response to flow was developed in Chapter 4 using DWA historical monitoring data. The model was verified as accurate in certain case studies using observed point loading information. In Chapter 5, statistical models that link land cover information to diffuse nutrient signatures in response to flow using DWA historical data were developed. While the model estimations are uncertain due to a lack of data, they do provide an estimation of the diffuse signature within catchments where there is flow and land cover information available. Chapter 6 investigates the extension of an existing mass-balance salinity model to estimate the effect of saline irrigation return flow on in-stream salinity. The model gave accurate salinity estimates for a low order stream with little or no irrigation within its catchment, and for a permanently flowing river within a catchment used extensively for irrigation. Chapter 7 investigated a modelling method to estimate the reaction coefficients involved in nitrification using only DWA historical monitoring data. Here, the model used flow information to estimate the residence time of nutrients within the studied river reaches. While the model obtained good estimations of nitrification for the data it was applied to, very few DWA data sets were suitable for the model. Chapter 8 investigated the ability of the in-stream model QUAL2K to estimate nutrient concentrations downstream of point and diffuse inputs of nutrients. It was found that the QUAL2K model can give accurate results in cases where point sources dominate the total nutrient inputs into a river. However, the QUAL2K simulations are too uncertain in cases where there are large diffuse source inputs of nutrients as the load of the diffuse inputs is difficult to measure in the field. This research highlights the problem of data scarcity in terms of temporal resolution as well as the range of constituents measured within DWA historical monitoring data for water quality. This thesis in addition argues that the approach of applying a number of models is preferable to applying one model to investigate the research aims, as particular models would be suited to particular circumstances, and the development of new models allowed the research aims of this thesis to be explored more thoroughly. It is also argued that simpler models that simulate a few key processes that explain the variation in observed data, are more suitable for implementing Integrated Water Resource Management (IWRM) than large comprehensive water quality models. From this research, it is clear that simple statistical models are not adequate for modelling the relationship between flow and water quality, however, relatively simple mechanistic models that simulate a limited number of processes and water quality variables, can provide accurate representations of this relationship. Under conditions where diffuse sources are not a major factor within a catchment, models that omit diffuse sources can obtain realistic simulations of the relationship between flow and water quality. Most of the models investigated in this thesis demonstrate that accurate simulations of the relationships between flow and water quality can be obtained using solely historical monitoring data.

The thesis presents the development of functionalized electrospun nylon 6 nanofibers for the eradication of pathogenic microorganisms in drinking water. Imidazole derivatives were synthesized as the antimicrobial agents and were characterized by means of NMR spectroscopy, IR spectroscopy, elemental analysis and X-ray crystallography. The first set of compounds (2-substituted N-alkylimidazoles) consisted of imidazole derivatives substituted with different alkyl groups (methyl, ethyl, propyl, butyl, heptyl, octyl, decyl and benzyl) at the 1-position and various functional groups [carboxaldehyde (CHO), alcohol (CH2OH) and carboxylic acid (COOH)] at the 2-position. It was observed that the antimicrobial activity of the compounds increased with increasing alkyl chain length and decreasing pKa of the 2-substituent. It was also observed that the antimicrobial activity was predominantly against a Gram-positive bacterial strains [Staphylococcus aureus (MIC = 5-160 μg/mL) and Bacillus subtilis subsp. spizizenii (MIC = 5-20 μg/mL)], with the latter being the more susceptible. However, the compounds displayed poor antimicrobial activity against Gram-negative bacterial strain, E. coli (MIC = 150- >2500 μg/mL) and did not show any activity against the yeast, C. albicans. The second set of compounds consisted of the silver(I) complexes containing 2-hydroxymethyl-N-alkylimidazoles. The complexes displayed a broad spectrum antimicrobial activity towards the microorganisms that were tested and their activity [E. coli (MIC = 5-40 μg/mL), S. aureus (MIC = 20-80 μg/mL), Bacillus subtilis subsp. spizizenii (MIC = 5-40 μg/mL) and C. albicans (MIC = 40-80 μg/mL)] increased with the alkyl chain length of the 2-hydroxymethyl-N-alkylimidazole. The third set of compounds consisted of the vinylimidazoles containing the vinyl group either at the 1-position or at the 4- or 5- position. The imidazoles with the vinyl group at the 4- or 5-position contained the alkyl group (decyl) at the 1-position. For the fabrication of the antimicrobial nanofibers, the first two sets of imidazole derivatives (2-substituted N-alkylimidazoles and silver(I) complexes) were incorporated into electrospun nylon 6 nanofibers while the third set (2-substituted vinylimidazoles) was immobilized onto electrospun nylon 6 nanofibers employing the graft polymerization method. The antimicrobial nylon nanofibers were characterized by IR spectroscopy and SEM-EDAX (EDS). The electrospun nylon 6 nanofibers incorporated with 2-substituted N-alkylimidazoles displayed moderate to excellent levels of growth reduction against S. aureus (73.2-99.8 percent). For the electrospun nylon 6 nanofibers incorporated with silver(I) complexes, the levels of growth reduction were >99.99 percent, after the antimicrobial activity evaluation using the shake flask method. Furthermore, the grafted electrospun nylon 6 nanofibers showed excellent levels of growth reduction for E. coli (99.94-99.99 percent) and S. aureus (99.93-99.99 percent). The reusability results indicated that the grafted electrospun nylon 6 nanofibers maintained the antibacterial activity until the third cycle of useage. The cytotoxicity studies showed that grafted electrospun nylon 6 nanofibers possess lower cytotoxic effects on Chang liver cells with IC50 values in the range 23.48-26.81 μg/mL. The thesis demonstrated that the development of antimicrobial electrospun nanofibers, with potential for the eradication of pathogenic microoganisms in water, could be accomplished by incorporation as well as immobilization strategies.

This study contributes a procedure, based on data analysis and geostatistical methods, to evaluate the distribution of chemical ratios and differentiate natural and anthropogenic contaminant sources of groundwater quality in the East Texas Basin. Four aquifers were studied, Sparta, Queen City, Carrizo and Wilcox. In this study, Carrizo- Wilcox is considered as one aquifer, and Sparta-Queen City as another. These aquifers were divided into depth categories, 0-150 feet for Sparta-Queen City and 300-600 feet and 600-900 feet for Carrizo-Wilcox in order to identify individual sources of contamination. Natural sources include aquifer mineral make up, salt domes and lignite beds. Major anthropogenic sources include lignite and salt dome mining and oil-gas production. Chemical ratios selected were Na/Cl, Ca/Cl, Mg/Cl, SO4/Cl, (Na+Cl)/TDS, SO4/Ca and (Ca+Mg)/(Na+K). Ratio distributions and their relationships were examined to evaluate physical-chemical processes occurring in the study area. Potential contaminant sources were used to divide the Basin into three areas: Area 1 to the east, Area 2 in the west and Area 3 in the center. Bivariate analysis was used to uncover differences between the areas. The waters in Area 1 are potentially impacted primarily from oil field waters. Sources present in Area 2 include lignite beds and oil field operations. Area 3 is the cap rock of salt domes that can contain gypsum and anhydrite. Based on the exploratory data analysis (Na+Cl)/TDS, (Ca+Mg)/(Na+K), and SO4/Ca ratios were chosen for geostatistical analysis. Chemical ratios that provided indications of cation exchange, salt domes and oil fields were (Na+Cl)/TDS, (Ca+Mg)/(Na+K) and SO4/Ca. In the Sparta-Queen City 150 zone the procedure did not provide a good method for differentiating between contaminant sources. However, the procedure was effective to indicate impacted ground water in the Carrizo-Wilcox 600 and 900 foot zones.

The purpose of this study was to examine the suitability of the YSI model 6600 Environmental Monitoring System (multiprobe) for long term deployment at a site in Lewisville Lake, Texas. Specifically, agreement between a laboratory extraction procedure and the multiprobe chlorophyll/fluorescence readings was examined. Preliminary studies involved determining the best method for disrupting algal cells prior to analysis and examining the precision and linearity of the acetone extraction procedure. Cell disruption by mortar and pestle grinding was preferable to bath sonication. Comparison of the chlorophyll/fluorescence readings from the multiprobe and the extraction procedure indicated that they were significantly correlated but temperature dependent.

Storm water quality can have a significant impact on receiving water bodies. The chief recipients of these impacts are aquatic life in the receiving water body and downstream water users. Over the last few decades, legislation, regulations, institutions and facilities have evolved to recognize the impact of urban storm water on receiving streams. This increased emphasis has caused contaminants in storm water to be identified as a major concern. This developing concern has generated an increased interest in the water quality of our streams and lakes and emphasized the need for more monitoring efforts. With the passage of the National Pollutant Discharge Elimination System (NPDES) Phase II requirements, small municipalities are responsible for storm water impacts on receiving waters within their jurisdiction. For the purposes of NPDES Phase II requirements, small municipalities are identified as these municipalities that are typically composed of 10,000 but less than 100,000 in population. The purpose of this dissertation is to develop a manual for use by the staff of small municipalities in meeting the requirements prescribed by changes initiated in the NPDES Phase II regulations. Attempts were made to comply with these requirements within a very limited manpower and budget framework and to develop procedures that would allow for permit compliance using testing equipment that was both reliable and robust. The users' manual provides valuable guidance in the establishment of a knowledge base for characterization of the watersheds selected for study. Chapter 3 of the dissertation contains a users' manual, designed for use by municipal staff members in their efforts to comply with the NPDES Phase II requirements. Using the techniques and equipment capabilities developed during the writing of the users' manual a characterization of three watersheds within Denton County, Texas was developed. Non-storm water samples were taken from each of the streams and a baseline analysis was established. The three watersheds represented agricultural, suburban and urban settings. Storm water samples were obtained from multiple storms within all three watersheds and data analysis used to determine the character and impact of urban runoff. Determination of the constituents for analysis was based on monitoring requirements of the NPDES Phase I and II requirements for owners and operators of municipal separate storm sewer systems (MS4) and on the Texas Pollutant Discharge Elimination System (TPDES) Multi-Sector General Permit (MSGP). The three watersheds were determined to have multiple statistically significant differences for some parameters between their Base Flows and Storm Flows. The impact of urban runoff on the receiving waters of these three drainage systems was clearly demonstrated throughout the testing period.

The South Slough Estuary is located off Coos Bay along the southern coast of Oregon. It is divided into two channels that meet and continue to Coos Bay at the Charleston Harbor. There are six major contributing streams to South Slough. After rainfall events, the level of coliform bacteria in the slough increases because of stream bacteria loading. This is due to cattle grazing in the drainage areas, failed septic systems from private homes, and sewage sludge applied to the County landfill, which drains into the slough. The Oregon Health Division has enforced a Sanitation Management Plan for Commercial Shellfish Harvesting in South Slough that specifies closure of commercial shellfish harvesting for certain rainfall and flood events. The purpose of this study is to analyze and improve the current understanding of the hydraulics and water quality of the South Slough Estuary. This was achieved by calibrating the South Slough using the water quality model CEQUAL- W2. It was calibrated for the following parameters water surface elevations, velocity, temperature and total dissolved solids. A management analysis was also done analyzing the transport of bacteria and a conservative tracer. Model predictions for water surface elevations at one of the monitoring sites, Hinch Road Bridge, was significantly lower than measured elevations. There was an excellent correlation of velocity, and reasonable timing of peaks due to tidal effects. Model predictions for temperature and total dissolved solids match measured values well. To improve the accuracy of the model the following was recommended; install a raingage in the South Slough, measure temperature and constituent concentrations at inflow locations, survey the S4 current meter, new soundings performed of the Winchester Creek arm and at the Hinch Road Bridge gaging station, and investigate the possibility of an obstruction near the Hinch Road Bridge gaging station.

Algal blooms plague freshwaters across the globe, as increased nutrient loads lead to eutrophication of inland waters and the presence of potentially harmful cyanobacteria. In this context, remote sensing is a valuable approach to monitor water quality over broad temporal and spatial scales. However, there remain several challenges to the accurate retrieval of water quality parameters, and the research in this thesis investigates these in an optically complex lake (Lake Balaton, Hungary). This study found that bulk and specific inherent optical properties [(S)IOPs] showed significant spatial variability over the trophic gradient in Lake Balaton. The relationships between (S)IOPs and biogeochemical parameters differed from those reported in ocean and coastal waters due to the high proportion of particulate inorganic matter (PIM). Furthermore, wind-driven resuspension of mineral sediments attributed a high proportion of total attenuation to particulate scattering and increased the mean refractive index (n̅p) of the particle assemblage. Phytoplankton pigment concentrations [chlorophyll-a (Chl-a) and phycocyanin (PC)] were also accurately retrieved from a times series of satellite data over Lake Balaton using semi-analytical algorithms. Conincident (S)IOP data allowed for investigation of the errors within these algorithms, indicating overestimation of phytoplankton absorption [aph(665)] and underestimation of the Chl-a specific absorption coefficient [a*ph(665)]. Finally, Chl-a concentrations were accurately retrieved in a multiscale remote sensing study using the Normalized Difference Chlorophyll Index (NDCI), indicating hyperspectral data is not necessary to retrieve accurate pigment concentrations but does capture the subtle heterogeneity of phytoplankton spatial distribution. The results of this thesis provide a positive outlook for the future of inland water remote sensing, particularly in light of contemporary satellite instruments with continued or improved radiometric, spectral, spatial and temporal coverage. Furthermore, the value of coincident (S)IOP data is highlighted and contributes towards the improvement of remote sensing pigment retrieval in optically complex waters.

Os corpos hídricos estão entre os ambientes mais prejudicados pelo crescimento desordenado da população humana. Considerando-se a grande importância de rios e lagos, tanto para os organismos residentes, quanto para a saúde da população humana, são necessárias estratégias que incluam, concomitantemente, a produtividade e a sustentabilidade em um mesmo ambiente, visando o equilíbrio ecológico. Assim, o presente trabalho teve como objetivo avaliar diferentes tipos de poluição ao longo do Rio Jirau Alto, no município de Dois Vizinhos, PR, por meio de biomarcadores genéticos em peixes da espécie Astyanax bifasciatus, em duas estações do ano (verão e inverno). Foram empregados o teste de Alterações morfológicas nucleares (ENA) associado ao teste de micronúcleos e Ensaio Cometa em sangue e fígado como biomarcadores genéticos. As coletas foram realizadas em duas estações (verão e inverno de 2016) em quatro pontos amostrais ao logo do rio Jirau alto, e um ponto controle em uma APP. Os biomarcadores empregados foram o ensaio cometa com eritrócitos e hepatócitos, e frequência de alterações morfológicas nucleares (ENA). O teste de micronúcleo písceo foi utilizado para determinar as quebras irreversíveis nos cromossomos de eritrócitos dos peixes e também alterações morfológicas nucleares de vários tipos. O ensaio cometa é uma técnica bastante eficiente nos estudos de agentes tóxicos que causam danos ao material genético, e por sua vez permite quantificar as quebras de DNA. Os resultados obtidos demostraram evidências de contaminação nesse rio, os dados obtidos pelo teste de micronúcleo mostraram danos elevados, em todos os pontos amostrais quando comparados ao ponto controle, em ambas as estações. No teste de ensaio cometa, os valores de danos estiveram mais elevados, principalmente no verão e se mostrando com maior significância especialmente no ponto P2. No entanto, essa resposta foi não linear, evidenciando variações também entre os pontos e estações. Assim, pesquisas de monitoramento se tornam indispensáveis para a avaliação dos efeitos da poluição ambiental sendo necessária a conscientização da população, devido a ameaça de contaminação nesse rio, uma vez que desempenha papel importante no abastecimento público da cidade de Dois Vizinhos. / The water bodies are among the environments most affected by the disorderly growth of the human population. Considering the great importance of rivers and lakes, both for the resident organisms and for the health of the human population, strategies are needed that include, simultaneously, productivity and sustainability in the same environment, aiming at ecological balance. The objective of this work was to evaluate different types of pollution along the Jirau Alto River, in the municipality of Dois Vizinhos, PR, by means of genetic biomarkers in fish of the species Astyanax bifasciatus, in two seasons of the year (summer and winter). The Nuclear Morphological Changes (ENA) test associated with the micronucleus test and the Comet Assay in blood and liver were used as genetic biomarkers. The collections were carried out in two seasons (summer and winter of 2016) at four sampling points at the Jirau Alto river, and one control point at an APP. The biomarkers employed were the comet assay with erythrocytes and hepatocytes, and frequency of nuclear morphological changes (ENA). The micronucleus test was used to determine irreversible chromosome breaks in fish erythrocytes as well as nuclear morphological changes of various types. The comet assay is a very efficient technique in studies of toxic agents that cause damage to the genetic material, and in turn allows quantification of DNA breaks. The results obtained showed evidence of contamination in this river, the data obtained by the micronucleus test showed high damages, in all the sampling points when compared to the control point, in both stations. In the comet test, damage values were higher, especially in the summer and showing more significance especially at point P2. However, this response was non-linear, evidencing variations also between points and seasons. Thus, monitoring research becomes indispensable for the evaluation of the effects of environmental pollution and it is necessary to raise awareness of the population due to the threat of contamination in this river, since it plays an important role in the public supply of the city of Dois Vizinhos.

Os corpos hídricos estão entre os ambientes mais prejudicados pelo crescimento desordenado da população humana. Considerando-se a grande importância de rios e lagos, tanto para os organismos residentes, quanto para a saúde da população humana, são necessárias estratégias que incluam, concomitantemente, a produtividade e a sustentabilidade em um mesmo ambiente, visando o equilíbrio ecológico. Assim, o presente trabalho teve como objetivo avaliar diferentes tipos de poluição ao longo do Rio Jirau Alto, no município de Dois Vizinhos, PR, por meio de biomarcadores genéticos em peixes da espécie Astyanax bifasciatus, em duas estações do ano (verão e inverno). Foram empregados o teste de Alterações morfológicas nucleares (ENA) associado ao teste de micronúcleos e Ensaio Cometa em sangue e fígado como biomarcadores genéticos. As coletas foram realizadas em duas estações (verão e inverno de 2016) em quatro pontos amostrais ao logo do rio Jirau alto, e um ponto controle em uma APP. Os biomarcadores empregados foram o ensaio cometa com eritrócitos e hepatócitos, e frequência de alterações morfológicas nucleares (ENA). O teste de micronúcleo písceo foi utilizado para determinar as quebras irreversíveis nos cromossomos de eritrócitos dos peixes e também alterações morfológicas nucleares de vários tipos. O ensaio cometa é uma técnica bastante eficiente nos estudos de agentes tóxicos que causam danos ao material genético, e por sua vez permite quantificar as quebras de DNA. Os resultados obtidos demostraram evidências de contaminação nesse rio, os dados obtidos pelo teste de micronúcleo mostraram danos elevados, em todos os pontos amostrais quando comparados ao ponto controle, em ambas as estações. No teste de ensaio cometa, os valores de danos estiveram mais elevados, principalmente no verão e se mostrando com maior significância especialmente no ponto P2. No entanto, essa resposta foi não linear, evidenciando variações também entre os pontos e estações. Assim, pesquisas de monitoramento se tornam indispensáveis para a avaliação dos efeitos da poluição ambiental sendo necessária a conscientização da população, devido a ameaça de contaminação nesse rio, uma vez que desempenha papel importante no abastecimento público da cidade de Dois Vizinhos. / The water bodies are among the environments most affected by the disorderly growth of the human population. Considering the great importance of rivers and lakes, both for the resident organisms and for the health of the human population, strategies are needed that include, simultaneously, productivity and sustainability in the same environment, aiming at ecological balance. The objective of this work was to evaluate different types of pollution along the Jirau Alto River, in the municipality of Dois Vizinhos, PR, by means of genetic biomarkers in fish of the species Astyanax bifasciatus, in two seasons of the year (summer and winter). The Nuclear Morphological Changes (ENA) test associated with the micronucleus test and the Comet Assay in blood and liver were used as genetic biomarkers. The collections were carried out in two seasons (summer and winter of 2016) at four sampling points at the Jirau Alto river, and one control point at an APP. The biomarkers employed were the comet assay with erythrocytes and hepatocytes, and frequency of nuclear morphological changes (ENA). The micronucleus test was used to determine irreversible chromosome breaks in fish erythrocytes as well as nuclear morphological changes of various types. The comet assay is a very efficient technique in studies of toxic agents that cause damage to the genetic material, and in turn allows quantification of DNA breaks. The results obtained showed evidence of contamination in this river, the data obtained by the micronucleus test showed high damages, in all the sampling points when compared to the control point, in both stations. In the comet test, damage values were higher, especially in the summer and showing more significance especially at point P2. However, this response was non-linear, evidencing variations also between points and seasons. Thus, monitoring research becomes indispensable for the evaluation of the effects of environmental pollution and it is necessary to raise awareness of the population due to the threat of contamination in this river, since it plays an important role in the public supply of the city of Dois Vizinhos.

Internationally, water resources are facing increasing pressure due to over-exploitation and pollution. Integrated Water Resource Management (IWRM) has been accepted internationally as a paradigm for integrative and sustainable management of water resources. However, in practice, the implementation and success of IWRM policies has been hampered by the lack of availability of integrative decision support tools, especially within the context of limited resources and observed data. This is true for the Crocodile River Catchment (CRC), located within the Mpumalanga Province of South Africa. The catchment has been experiencing a decline in water quality as a result of the point source input of a cocktail of pollutants, which are discharged from industrial and municipal wastewater treatment plants, as well as diffuse source runoff and return flows from the extensive areas of irrigated agriculture and mining sites. The decline in water quality has profound implications for a range of stakeholders across the catchment including increased treatment costs and reduced crop yields. The combination of deteriorating water quality and the lack of understanding of the relationships between water quantity and quality for determining compliance/non-compliance in the CRC have resulted in collaboration between stakeholders, willing to work in a participatory and transparent manner to create an Integrated Water Quality Management Plan (IWQMP). This project aimed to model water quality, (combined water quality and quantity), to facilitate the IWQMP aiding in the understanding of the relationship between water quantity and quality in the CRC. A relatively simple water quality model (WQSAM) was used that receives inputs from established water quantity systems models, and was designed to be a water quality decision support tool for South African catchments. The model was applied to the CRC, achieving acceptable simulations of total dissolved solids (used as a surrogate for salinity) and nutrients (including orthophosphates, nitrates +nitrites and ammonium) for historical conditions. Validation results revealed that there is little consistency within the catchment, attributed to the non-stationary nature of water quality at many of the sites in the CRC. The analyses of the results using a number of representations including, seasonal load distributions, load duration curves and load flow plots, confirmed that the WQSAM model was able to capture the variability of relationships between water quantity and quality, provided that simulated hydrology was sufficiently accurate. The outputs produced by WQSAM was seen as useful for the CRC, with the Inkomati-Usuthu Catchment Management Agency (IUCMA) planning to operationalise the model in 2015. The ability of WQSAM to simulate water quality in data scarce catchments, with constituents that are appropriate for the needs of water resource management within South Africa, is highly beneficial.