A research report submitted to the Faculty of Engineering and the Built Environment, University of the Witwatersrand, Johannesburg, in partial fulfillment of the requirements for the degree of Master of Science in Engineering Johannesburg, 2018 / The main objective of this report is to assess the effect of different topographic (elevation) data sources on river habitat modelling in low flow conditions. In the study, digital terrain models which consists of various datasets were assessed using 2-D hydraulic software models. The representation of the terrain was sourced from the following: airborne laser scanning, total station survey, a smartphone device and a handheld GPS device. From the results, which consisted of 4 simulations (discharges of 1.5 m3/s, 1 m3/s, 0.5 m3/s, and a field measurement of 0.3 m3/s) for each topographic dataset, the water level and velocity were derived and a comparison was made against the most accurate data set (total station survey). The comparisons included how each model was able to describe a habitat in terms of defined biotopes. This research proves that a total station survey is still the most accurate, however with the advancement in GPS technology a handheld GPS device has proven to be adequate for a desktop or intermediate study. In addition, a smartphone’s GPS tends to be more adequate for large surveys and inefficient for habitat modelling. / MT 2018

This thesis develops a technique for the identification, classification and quantification of instream flow environments. These features have been traditionally referred to as 'habitats' by lotic ecologists, in this research they are termed 'hydraulic biotopes'. The hydraulic biotope is the lowest of six nested levels of a hierarchical geomorphological model. This model has been developed as a tool to assist river managers, researchers and conservationists to categorise or classify rivers with respect to their geomorphic characteristics. Each level of the model provides data at a different level of resolution. This ranges from the broad scale catchment data to the site specific 'habitat' or hydraulic biotope data. Although this thesis is primarily concerned with the development of the hydraulic biotope, the interaction of all catchment variables needs to be recognised. Detailed analysis of hydraulic biotope data in the Buffalo River are presented within the broader hierarchical model. Consultation with lotic ecologists, together with a review of ecological literature, emphasised the need for a standardised terminology for the classification of ecologically significant instream flow environments. At present a fairly haphazard 'habitat' classification tends to be carried out by most researchers, this often leads to confusion in the identification and naming of different hydraulic biotopes ('habitats'). This confusion is exaggerated by the sharing of terminology between lotic ecology and fluvial geomorphology, usually for the categorisation of different types of features. A review of the ecological literature emphasises the importance of flow hydraulics within a river to describe the distribution of biota. The hydraulic variables considered to be most significant include velocity and depth. As river morphology directly determines the prevailing distribution of depth, velocity and substratum, it is obvious that there are important links to be made between fluvial geomorphology and lotic ecology. This thesis explores the potential of the hydraulic biotope as a tool to help develop those links. This thesis presents a standardised classification matrix for the identification of hydraulic biotopes. The matrix is simply based on water surface characteristics together with channel bed substratum. The validity of this matrix is tested by statistical analysis of hydraulic variables quantifying flow conditions within the various hydraulic biotope classes. Data is presented from four different river systems, each representing a different sedimentological environment. Where possible the influence of discharge has been considered. Results from more than 3000 data points show that hydraulic biotopes have distinct hydraulic characteristics in terms of velocity-depth ratio, Froude number, Reynolds number, 'roughness' Reynolds number and shear velocity. These hydraulic indices represent flow conditions both as an average within the water column, and near the bed. Statistical analysis shows that the hydraulic characteristics of the various hydraulic biotope classes are relatively consistent both within different fluvial environments and at different stages of flow. Unlike the morphological unit in which the hydraulic biotope is nested, in stream flow environments are shown to be temporally dynamic. Using the classification matrix as a tool for identification, hydraulic biotopes identified at one discharge are shown to be transformed from one class to another as a response to change in stage. The pattern of transformation is shown to be consistent within different sedimentological environments. An examination of the associations between hydraulic biotopes and morphological units demonstrates that, although some hydraulic biotopes are common to all morphological units (backwater pools, pools and runs), some features have specific associations. In this study rapids were found to be prevalent in bedrock pavement, bedrock pool and plane bed morphology, while cascades, chutes and riffles were common to plane bed, step and riffle morphology. Results from this research indicate that the hydraulic biotope, within the hierarchical geomorphological model, has the potential to aid the prediction of channel adjustment and associated 'habitat' (hydraulic biotope) transformation in response to changes in flow and sediment yield. These are likely to become increasingly important issues as South Africa strives to maintain a balance between the development of water resources to meet the needs of the rapidly expanding population, whilst at the same time maintaining the fluvial environment for sustainable use.

Ferreira, M., Dr.; Van Vuren, J.H.J., Prof. / The Wilge River is one of many adjoining tributaries of the Olifants River located in the Olifants Water Management Area (WMA4) within the Highveld (11) – Lower Level 1 Ecoregion (Dallas, 2007). These river systems experience extreme demand for natural resources, as they flow through heavily utilised economic hubs. They are closely associated with land modification and pollution, primarily mining and industrial-related disturbances and extensive agricultural activities, all of which are the primary cause of impairment to river health. The primary aim of this study was to study the aquatic macroinvertebrate communities at six monitoring sites along the Wilge River, coupled with two monitoring sites on adjoining tributaries, and to further identify the driving variables that influence these communities both spatially and temporally. Functional Feeding Groups (FFGs) of the aquatic macroinvertebrates and the surrounding land use in the project area was taken into account. The analysis of in situ water quality measured during the period March 2010 to May 2013, clearly illustrated high levels of variation both spatially and temporally. In situ water quality was a limiting factor to the aquatic ecosystem from a Dissolved Oxygen (DO) and Percentage Saturation (DO%) perspective. The remaining parameters were within the South African guideline for aquatic ecosystems (DWAF, 1996). Habitat availability illustrated clear seasonal variation as well, of which the wet season indicated better habitat availability compared to the dry season. The dominant biotopes in the study area were vegetation (VEG) and gravel, sand and mud (GSM). Site WIL04 illustrated the poorest habitat integrity overall primarily attributed to the site’s steep incised banks and deep channel which lacks the stones biotope. The South African Scoring System, Version 5 (SASS5) results indicated that there was a change in the integrity of the aquatic macroinvertebrate community’s in the study area and further illustrated variability both spatially and temporally. It was evident that the aquatic macroinvertebrate communities within the Wilge River and two adjoining tributaries sampled, were generally in a slightly to modified state with moderate variations. The lowest number of taxa, SASS5 and average score per taxon (ASPT) values was recorded at site WIL04 and this was mainly brought about due to changes in flow and habitat availability. The ASPT score ranged from 3.8 at site WIL04 to 7.7 at site WIL02, indicating that the aquatic macroinvertebrate communities were primarily composed of tolerant and moderately tolerant taxa. Of these mostly tolerant taxa, predators and gathering collector populations were the most dominant FFG, with the shredders being the least abundant within the study area. The Bray-Curtis cluster analysis of the aquatic macroinvertebrate communities clearly illustrated a high level of similarity and seasonal variation among the communities. The high similarity was an indication that similar taxa occurred at the sites within the groups identified. However, in accordance with the Similarity Percentages (SIMPER) analysis, there was no clear indication of dominant taxa. There was however a separation of sites TRI01 and WIL04. This was expected due to differences in the physical stream condition (flow) and other habitats / general biotopes, primarily at site WIL04. Stream bed composition is one of the most important physical factors controlling the structure of freshwater invertebrate communities (Mackay and Eastburn, 1990). The separation and similarity of these two sites were not a consequence of dominant taxa, but rather a consequence of differing water quality, habitat availability and common tolerant taxa driving the system. Inclusive, the seasonal variation illustrated was contributing to the changes in the in situ water quality and habitat availability, thus making seasonal variation also a driving variable, in the differences between the sites. The Redundancy Analysis (RDA) bi-plots indicated, as with the Bray-Curtis similarity matrices and related NMDS plot, that there was a distinct seasonal separation. It further illustrated a clear separation of site TRI01 and WIL04 due to reasons mentioned above. All the environmental variables, with the exception of pH, was identified as significant drivers in the river systems (p<0.05). This however varied seasonally. During the wet season, clarity, DO and pH were the significant drivers, while clarity, TDS/EC, percentage saturation and pH were the significant drivers during the dry season (p<0.05). These drivers were expected due to possible sources namely intensive agriculture in the project area. The RDA tri-plots further indicated the significant role that the ASPT, SASS5 score and the IHAS played within the aquatic macroinvertebrate community (p<0.05). This confirms the importance of habitat as a driving variable in aquatic macroinvertebrate community structures. Consequently, the driving variables in the separation of the sites along the Wilge River and two adjoining tributaries, appear to be a combination of variables (DO, percentage saturation, TDS/EC, clarity and pH), including habitat availability (based on IHAS scores). To determine the effects and relations between the primary driving changes, to the surrounding land uses in the project area, further multivariate analyses were conducted, which included the FFGs. It was clearly indicated that predators have a negative correlation with the rest of the FFG’s which was expected. As the percentage of predators increase at a site, the percentage of the other FFG’s decreased. Therefore, there was a large variation and clear changes in the food sources constantly entering into the river system. This is normally related to changes in the land use.

This thesis examines the extent and intensity of the effects of impoundments on selected physical, chemical and biotic conditions in an impounded southern African river. Life-history characteristics and environmental requirements which determine the success of impoundment-outlet blackflies in southern Africa were studied. Difficulties with the identification of immature blackflies led to a search for additional diagnostic characters, the description of larvae of seven species previously unknown, and the development of new keys to the species of Simulium (larvae and pupae) in southern Africa. Distribution records for each species are presented, and their ecology is summarised. Three pairs of closely related species, which were formerly indistinguishable, can now be recognised by differences between the structure of their cephalic fan microtrichia. Monthly physical, chemical and invertebrate samples at 16 sites upstream and downstream of four impoundments in the Buffalo River, eastern Cape, were taken over a period of two years. The downstream effects of impoundments on these parameters depended on the variable examined, the position of the impoundment along the river profile, the depth from which water was released, and the quality of the inflowing water. Impoundments in the Buffalo River caused an upstream shift of the thermal and suspended organic conditions, and the distribution of blackfly species. Surface-release impoundments in the clean, upper-reaches of the river caused increases in water temperature (by as much as 8ºC) and chlorophyll a (by as much as 600%). Recovery to riverine conditions was within 2.6 to 18.4 km, depending on flow. A polluted, surface-release impoundment in the middle-reaches of the river had a slight dampening effect on river temperatures, converted the particle size spectrum of the river from small (<80 μm) to large (250-1000 μm), and improved the water quality of the downstream reaches (with the exception of nitrate concentrations, which were higher in the tailwaters compared to inflowing water). An impoundment in the lower reaches caused reductions in maximum temperature of up to 6ºC when releasing water from the surface, and up to 16ºC when releasing water from the bottom. Bottom-released water carried high concentrations (36 to 190 g m³) of small (<5 μm) and largely inorganic (86 to 93%) material.Twenty species of blackflies were found in the Buffalo River, of which 18 were distinguishable as larvae. They were divided into those which were widespread (5 taxa), those restricted to waterfalls and mountain torrents (2 taxa), those found in the foothill stony run zone (6 taxa), and rare taxa (5 taxa). Impoundments in the Buffalo River did not alter population densities of blackfly larvae, but did alter blackfly species composition, favouring five species commonly found in mid-order streams in southern Africa (s. meduseaforme, S. hargreavesi, S. nigritarse, S. adersi and s. damnosum s.l.) at the expense of upper-reach species (s. rutherfoordi, S. letabum and s. impukane). These five species are regarded as typical of impoundment-outlets, and were small, multivoltine flies whose larvae shared a generalised cephalic fan microtrichial structure, consisting of a single row of moderately differentiated microtrichia. A strong relation was found between cephalic fan microtrichial structure and larval habitats: Taxa found in fast-flowing, clear water had a more complex fan structure compared to those found in slow-flowing, turbid water. It is concluded that impoundment-induced changes to hydrodynamics and transported material (food) are important factors which have changed the distribution of blackflies in southern Africa in recent times. These changes are more severe downstream of upper-reach impoundments than middle or lower-reach impoundments.

M.Sc. (Aquatic Health) / Aquatic ecosystems in rural South Africa have been impacted over many years by commercial and subsistence anthropogenic activities (DWAF, 2001). These impacts include commercial and subsistence farming, domestic use (e.g. washing of clothes, cars and bathing) and recreational use (e.g. fishing). In the northern parts of the Limpopo Province of South Africa (Vhembe District) the land use is primarily dominated by various agricultural activities and human settlements. Rivers in this region flow through mixed agricultural use, including commercial agriculture (tea and timber plantations) as well as subsistence farming and housing. Perennial rivers in this region include the Mutale, Mutshindudi and Tshinane rivers. These rivers are located in the Water Management Area 2 (WMA 2 Luvuvhu-Letaba) (Kleynhans, et al., 2007a). They are highland river systems, originating in the nearby Soutpansberg Mountain, and these rivers all form part of the larger drainage system of the Luvuvhu River, a tributary of the Limpopo River. The wetlands in the catchment of these rivers are also heavily utilised by the local communities (Working on Wetlands, 2013) used for grazing, sand mining and subsistence cultivation, thus providing a livelihood for the surrounding communities (SANBI, 2012). The aim of the study was to assess aspects of the biological integrity of the Mutale, Mutshindudi and Tshinane rivers. This study formed part of a larger study that included assessments of both abiotic and biotic aspects of these river systems. For this study, the focus was on assessing the fish community structure through the application of Fish Response Assessment Index (FRAI), riparian vegetation through the application of Vegetation Response Assessment Index (VEGRAI) and fish health aspects with special reference to liver and gonadal histopathology. Water quality parameters were found to be within the target water quality range for aquatic ecosystems. The results did however vary between upstream and downstream sampling sites. Similarly, compared to upstream sites, the FRAI showed the Mutale River to improve in fish community structure whereas the Tshinane and Mutshindudi rivers showed a decrease in the FRAI score. The VEGRAI results showed a decrease in EcoCondition in the Mutale and Mutshindudi rivers whereas the Tshinane indicated an increase. This can be attributed to land use change up to the edge of the river systems. Visual observation at the various study sites showed a definite localised impact of human activities on the beds and banks of many parts of the rivers. No histological alterations were identified in any of the gonadal or liver tissue of the Chiloglanis pretoriae (Shortspine suckermouth) (Van der Horst, 1931) and the fish were found to be in a healthy condition according to the selected parameters (gonads and livers) assessed. The fish community structure of the three rivers were found to be in a moderately to largely modified condition according to the ecological state categories calculated. However, the fish health assessment showed no histological alterations in the sampled fish. It is proposed that future studies investigate the influence of the domestic use of the rivers as well as attempt to quantify the impact of agriculture on the system.

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.

The Eastern Cape Karoo region is semi-arid with highly variable rainfall. This variability in rainfall sustains a mosaic of surface freshwater bodies that range from permanently to temporarily inundated. These waterbodies provide habitats for diverse invertebrate assemblages. The imminent hydraulic fracturing for shale gas has a potential to modify the water regime, with particular risk of salinisation. Accumulation of salts in freshwater wetlands results in loss of biodiversity, as invertebrate species shift from salt intolerant to salt tolerant species. This study therefore aims to expand on existing knowledge and provide new information on the distribution, diversity and structure of macroinvertebrate assemblages associated with various freshwater bodies in the region prior to shale gas exploration. Limnological and ecological aspects of thirty-three waterbodies (rivers, dams and depression wetlands) were investigated between November 2014 and March 2016. An experimental study on the effects of salinity on hatching success of branchiopod resting eggs was also included in the research. Rivers were characterised by high conductivity and depression wetlands by high turbidity, while dams had relatively higher pH than the other two waterbody types. In terms of global phosphorus interpretation guidelines, the results indicate that freshwater systems in the study region are predominantly eutrophic, indicating that agricultural run-off, particularly from livestock dung (goats, cattle and sheep), is an important source of phosphorus in the freshwater systems studied. Our results revealed new distribution records for branchiopod crustaceans in the Eastern Cape region, including the first record of Laevicaudata. Results showed that the sampled variables were unable to explain the variation in physicochemistry and invertebrate assemblage of several sites. Waterbody type, whether a depression wetland or a river, was the only factor that consistently showed an effect on the composition of both physicochemical data and invertebrate data. Depression wetlands ranged from completely bare to being extensively covered by macrophytes. Therefore, the effect of macrophyte cover in structuring macroinvertebrate assemblages was the focus of further investigation. The results indicated that the macrophyte cover gradient had little influence on the structure of the invertebrate assemblages in the depression wetlands, while only the presence/absence of vegetation significantly influenced the structure of the invertebrate assemblages in these systems. Surface area, dissolved inorganic nitrogen and pelagic chlorophyll-a were the environmental variables that best explained the variation in the macroinvertebrate assemblages among the sites. However, the differences in macroinvertebrate richness, abundance and distribution patterns among sites were only weakly influenced by local and regional environmental factors. These findings suggest that invertebrate in temporary wetland systems are adapted to the highly variable nature of temporary habitats, thus the influence of local variables is negligible. Results of the experimental study, on the effect of salinity on hatching success of branchiopod resting eggs, revealed that hatchling abundance and diversity of large branchiopods was significantly reduced at salinities of 2.5 g L−1 and above. Salt-tolerant taxa such as Copepoda and Ostracoda were the only ones to emerge in the highest salinity of 10 g L−1. Thus, should the region continue to experience increasing aridity and possible shale gas development, which all aggravate the salinisation problem, severe loss of branchiopod diversity (Anostraca, Laevicaudata, Spinicaudata and Notostraca) is likely to occur. This may lead to considerable decline in invertebrate diversity in the region, with cascading effects on food webs and ecosystem functions. The findings of this study can potentially be used in comparative studies on wetland invertebrate ecology in other semi-arid regions and in the formulation of policy and strategies for biodiversity conservation.

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.

M.Sc. (Zoology) / Sediment contamination occurs as a result of various anthropogenic activities; mainly through mining-, agricultural- and industrial practices. Many of the contaminants arising from these activities enter the aquatic system and precipitate from the surrounding water, binding to sediment particles. In the sediment compartment, these contaminants reach concentrations much higher than in solution with the overlying water. Even though the quality of the overlying water may prove acceptable in accordance to water quality uidelines, an aquatic system may still be at risk from the contaminated sediment. If the contaminated sediment were to be disturbed through flooding, bioturbation or changes in the water chemistry, these contaminants will desorb into the water column and as a result be detrimental to life forms in contact and dependent on that water source. Monitoring sediment has been a widespread initiative internationally and has led to the development of various sediment toxicity test methods, including different bioassays. This study focused on sediment bioassays such as the Phytotoxkit-F and Ostracodtoxkit-F, and the Diptera bioassay to assess the sediment quality of the Tweelopiespruit-Rietspruit-Bloubankspruit (TRB) river system in Gauteng, South Africa. This river is known to be impacted by acid mine drainage (AMD) since late August 2002. Exposure of the bioassays to river sediment from preselected sampling sites (Site 1, closest to the mine, to Site 6, furthest from the mine, and Site 7, the reference site) provided an eco-toxicological estimation of the acute toxicity emanating from contaminants in the sediment. Physico-chemical analyses revealed high concentrations of metals and other contaminants in the water and sediment. A general linear decrease in contaminant concentrations was observed from Site 1 to Site 6. The results from the bioassays displayed a similar trend, since there were greater sensitivities (mortalities and growth inhibition) to sediments sampled closer to the mine. Due to high levels of contamination in sediments, compared to the overlying water, and the potential impact on aquatic organisms, sediment toxicity monitoring should be a compulsory requirement for environmental studies in South Africa

M.Sc. Aquatic Health) / The Klip River runs past heavy urbanization and industrialization as a consequence it is possibly one of the most abused river systems in Gauteng and perhaps the country as a whole. Eight sites were selected along the course of the Klip River for biomonitoring purposes. The sites were selected to represent the upper, middle and lower reaches of the river, while sites representing point source pollution sources were also included. Various biomonitoring techniques have been included to determine the present ecological state of the Klip River. This includes biotic indices to assess the ecological integrity of the fish and invertebrate communities and the habitat. In addition, fish health was assessed using a variety of histological, biomarker and bioaccumulation based assessments. From the results it is evident that the sites on the Klip River represent the three main regions of a river including headwaters, middle reaches and a mature river. These natural changes in river ecology also caused natural variations in the habitat availability and the resultant biotic communities. There were, however, many changes not related to these natural variations but rather the numerous anthropogenic activities present on the river. The most noticeable change has occurred due to alteration in the flow regime. These changes are brought about by the many weirs and bridges in the system, return flow from the numerous settlements and agricultural activities and the various WWTW. These alterations in flow have caused serious erosion of the stream banks and may lead to siltation of the system. It is clear from the results of the sediment particle size analysis that there is an increase in the percentage contribution of medium and very fine sand below site 3. This is a good indication that the increased flow below the Olifantsvlei WWTW is already causing siltation. Ultimately this can lead to loss of riffle habitat within the river. These flow alterations have also caused an alteration to habitat availability and quality and as a result caused a modified invertebrate community. The macroinvertebrate community at all the sites (below site 1) consisted of taxa that are tolerant to pollution. This is also reflected in the poor SASS 5 and ASPT scores observed at the various sites. These tolerant organisms probably occur in the system due to an altered habitat template and a change in water quality. It is important to note that although the values obtained for the water quality variables are within the TWQR that the oxygen saturation at some sites decreased. These sites included the sites below the Olifantsvlei WWTW, after the confluence with the Rietspruit and the last monitoring site. The Fish Health Assessment Index scores were the highest at site 3 and decreased to site 8. This indicated that the fish condition improved from site 3 to site 8. However, there was a large variation in the index scores from the individual specimens. The results of this assessment cannot be compared to other studies as no fish health assessment index has been applied on the Klip River. This study will serve as a baseline assessment for future studies of the fish health of the Klip River. The results of the metal analysis in the fish muscle tissue indicated relatively low levels that correspond to levels measured by Kotze (1999) while still being lower than fish sampled from the polluted Olifants River. It is therefore recommended that further studies be completed on the fish health of the Klip River and that the fish health of specimens in the Klip River is compared to those of the Vaal River to determine the impact of the Klip River system on the Vaal River. As it has become clear that the Rietspruit also influences the water quality of the Klip River it is recommended that further studies be completed on the Rietspruit to determine the cause of the impacts. Because the histological alterations identified may be the result of a range of different biological and/or chemical stressors, it is difficult to assign specific causative agents for the various alterations identified. Based on the selected parameters investigated, the results show that fish in the Klip River appears to be in a relatively healthy condition and the organs seem to be in a functional state. Establishing a histology-based monitoring programme for fish health in the Klip River, by incorporating appropriate sample sizes and various fish species is recommended. Monitoring of biological responses for assessing the significance of pollutants has become a reasonable measurement in biomonitoring, and use of biomarker responses has played a significant role in this aspect. However, no biomarker has been validated as a unique tool to determine the effects of pollutants on organisms. Furthermore, it is necessary to understand how bioaccumulation and biomarkers relate to each other on exposure to specific pollutants and how it varies between species, to interpret the effects of pollutant exposure in both the field and laboratory. The results obtained in this study indicate that there are definite impacts on the entire system, although these have not altered fish biology and functionality to a large extent. However, sample size should be considered when evaluating individual biomarker responses, as a larger sample size will be more representative of the resident fish community’s response to the pollutants and other stressors. It is difficult to assign specific stressors for the various biomarker responses identified. It is recommended that further biomarker studies be undertaken on the Klip River to increase the level of confidence in the results obtained.