Thesis (MSc.) Zoology)) -- University of Limpopo, 2019 / In South Africa, a high anthropogenic demand of water for domestic, recreational, agricultural, urbanisation and industrial purposes has placed enormous pressure on freshwater resources and has led to a decline in water quality. In addition to measuring water quality variables, the health assessment index (HAI) advocated by AvenantOldewage and Swanepoel (1993), and modified by Crafford and Avenant-Oldewage (2009) by incorporating the inverted parasite index (IPI), and adapted further by Madanire-Moyo et al. (2012) who excluded the white blood cells counts, has been used as a rapid and inexpensive means of assessing and monitoring fish health and, in turn, the state of aquatic ecosystems. However, few studies have evaluated the latter approach in conjunction with other biomonitoring indices to assess the water quality of impoundments. Thus, the aim of this study was twofold. The first was to evaluate the HAI adapted by Madanire-Moyo et al. (2012) as a means to establish the health status of Oreochromis mossambicus (Peters, 1852) sampled from various impoundments based on a once-off survey. The second was to establish if the adapted HAI, in conjunction with selected biomonitoring indices and environmental variables, could describe monthly and seasonal fluctuations of O. mossambicus health. Once-off surveys were conducted between April and May 2016 at five impoundments. The Luphephe-Nwanedi Dam located in the upper catchment of the Limpopo River System and Rhenosterkop Dam situated in the Elands River, a tributary of the Olifants River System, served as control sites due to little or no anthropogenic activities occurring in their catchment areas. In addition, surveys were conducted at Loskop and Flag Boshielo dams and Phalaborwa Barrage situated in the main stem of the Olifants River for comparison purposes. The latter three impoundments were selected because they vary in water quality and pollution levels. Monthly surveys were carried out at Flag Boshielo Dam from February 2016 to February 2017 to establish if the biomonitoring tools and the quantification of water and sediment quality variables, could describe and predict seasonal fluctuations in the health of O. mossambicus. To this end, water quality variables were measured during each survey. Water and sediment samples were collected for analysis of nutrients and metals. Oreochromis mossambicus were collected using gill nets. Fish health was assessed using the adapted HAI that was based on observing parasite burden, haematocrit determination and anomalies in body tissues and organs in conjunction with determining gonad and iv hepato-somatic indices, the condition factor, blood glucose levels, microscopy analyses of fish gills and metal concentrations in fish muscle tissues. Water quality in terms of pH, total dissolved solids and electrical conductivity, nutrients and some aqueous and sediment metals exhibited significant differences (p ˂ 0.05) between impoundments surveyed with water quality from good to poor being in the order of: Luphephe-Nwanedi Dams ˂ Rhenosterkop Dam ˂ Loskop Dam ˂ Phalaborwa Barrage ˂ Flag Boshielo Dam. The HAI scores varied significantly (p ˂ 0.0001) between impoundments and substantiated water quality variables results during once off surveys, indicating that the health of fish from Flag Boshielo Dam were most affected when compared to the health of fish surveyed from the other impoundments. Findings from monthly surveys conducted at Flag Boshielo Dam indicated better conditions in terms of water quality variables during a period of high inflow as opposed to periods of low inflow. The HAI scores obtained for fish exhibited significant (p ˂ 0.0001) differences between the months surveyed and were found to be in agreement with the water quality findings, indicating that flow regimes and water quality of an impoundment have an impact on fish health. The condition and somatic indices findings did not seem to be sensitive enough to discriminate between the impoundments during the once off surveys. While during monthly surveys, these indices were significantly (p ˂ 0.0001) different between the months, showing to be affected by seasonal fluctuations. Knowledge of the HAI in conjunction with blood glucose levels, gill histopathology and the arithmetic mean thickness of gill epithelium (Har) best described the health of fish in both the once off and monthly surveys. In conclusion, the findings of this study emphasised the HAI premise that fish from more polluted sites would be more impacted as opposed to less impacted sites, making the HAI adapted by Madanire-Moyo et al. (2012) an effective and rapid biomonitoring tool that can be used in the field. Furthermore, this study proved that the HAI can be used either solely or in association with the parasite index (PI) or IPI depending on the objectives of the study, as no pronounced differences were evident when using HAI, HAI with PI and HAI with IPI. / National Research Foundation (NRF) and Water Research Commission (WRC)

Interest in the subject of fish welfare is continuing to grow, with increasing public awareness and new legislation in the UK. Water quality has long been recognised as being of prime importance for welfare: water provides the fish with oxygen and removes and dilutes potentially toxic waste metabolites. This thesis investigates the interactions between water quality and the welfare of farmed rainbow trout (Oncorhynchus mykiss Walbaum). A literature review was undertaken to identify current recommended water quality limits for the health and welfare of farmed rainbow trout. Contradictions in the literature regarding suggested ‘safe’ water quality limits were also identified, as were deficiencies in some of the methods used to arrive at conclusions for recommended limits. The literature relating to the effects of poor water quality on welfare were also reviewed. The review ends with a discussion about water quality monitoring in the context of on-farm welfare assessment and how the information might be used in such a scheme. A telephone survey of UK rainbow trout farmers was undertaken to ascertain the level of water quality monitoring currently conducted. Participants in this study accounted for over 80% of 2005 UK rainbow trout production. It was established that 54% of farmers monitored dissolved oxygen to some extent and 69% monitored temperature, the most commonly measured water quality parameters and among the most important for health, welfare and growth. Subsequent visits were made to a sample of the participants in the telephone survey to obtain more detailed information of the farming operations, such as frequency of water quality monitoring, retention of production data and slaughter methods. Monitoring water quality will be an integral part of any on-farm welfare assessment scheme, and while measuring some water quality parameters requires specialist equipment, farmers should be able to monitor the essential parameters, dissolved oxygen and temperature. Any on-farm welfare assessment scheme for rainbow trout should incorparate fish-based measures in addition to resource-based parameters in order to provide as complete an overview of trout welfare as possible. An epidemiological study was undertaken to investigate the current status of welfare on UK rainbow trout farms and to identify risk factors for welfare. Forty-four trout farms from throughout the British Isles were visited between July 2005 and April 2007, sampling a total of 3700 fish from 189 different systems. Farms were visited twice, once in winter and once in summer, to account for any seasonal differences in fish physiology and environmental conditions. Data were collected on a range of fish parameters, together with background information on the batch from which the fish originated. Particular emphasis was placed on water quality due to the potential effects this can have on welfare. The water in each system sampled was monitored for 24 hours, with measurements of dissolved oxygen, temperature, pH, specific conductivity and ammonia taken every 15 minutes. A welfare score was developed for each fish using a multifactorial method, combining data on the condition of the fins, the condition of the gills, the stress hormone cortisol, the splenosomatic index and the mortality levels for the population of fish in the system. Using this welfare score and the individual components of the score as response variables, multi-level models were developed using the water quality, system and husbandry data collected. The primary risk factor that was associated with deteriorating welfare was disease. The purpose for which the fish was being farmed was also important, as fish farmed for the table market had on average worse welfare than those farmed for restocking fisheries. Seasonal effects, linked to higher water temperatures in summer, were associated with poorer welfare scores. Aside from seasonal effects, there is not much evidence that poor water quality is a major problem for the welfare of farmed rainbow trout in the UK. While deteriorating water quality certainly has the potential to affect the welfare of farmed rainbow trout, water quality measurements were within recommended ranges for the majority of farms visited. The results of this epidemiological study suggest that factors other than water quality may have a greater impact on trout welfare, such as exposure to diseases and production differences between farming for the table and restocking markets.

This study assessed the quality of the Umgeni River in Durban South Africa seasonally from March 2011 to January 2012, according to standard protocol. Water samples were collected from Inanda dam-U5, KrantzKloof Nature Reserve-U4, New Germany-U3, Reservoir Hills –U2 and River mouth – U1 areas of the Umgeni River. A two-step tangential flow filtration (TFF) process was setup for the concentration of viruses from water samples. Virus like particles (VLPs) was detected using electron microscopy. Canonical correspondence analysis (CCA) was used to statistically evaluate the data sets. All water samples had turbidity values which exceeded the South African water quality guideline value of 0.1 NTU for turbidity. Large seasonal variations in BOD5, COD and conductivity levels were observed. Chloride concentrations were extremely high at point U1 (19234 mg/ℓ) Cl during summer. Total heterotrophic bacterial (THB) population was highest at 13.67 x 106 cfu/100ml (U1 – summer). Enterococci (EC) concentrations were detected at points U1, U2, U3, and U4 during the autumn and spring period. pH, electrical conductivity, temperature, and turbidity positively correlated with the microbial communities, and were the key parameters responsible for water pollution according to CCA. Most water samples contained high populations of somatic (659 pfu/mℓ, U1 – summer) and F-RNA coliphages (550 pfu/mℓ, U2 – summer). VLPs were detected throughout all seasons, with point U1 (summer) having the highest population of 2086 VLP/mℓ. Several presumptive viruses including Adenoviridae, Picornaviridae, Poxviridae, and Reoviridae were detected based on their morphologies. Six cell culture lines were used to determine cytopathic effect (CPE) of the VLPs. VLP samples produced CPEs on the Vero, Hek 293, Hela and A549 cell lines. Integrated cell culture (ICC) - PCR confirmed the presence of infectious VLPs in the river water samples. Adenoviruses, Enteroviruses, rotaviruses and Hepatitis B viruses were detected and quantified in all water samples by nested PCR/RT-PCR and Real-Time PCR respectively, against positive control viruses. These results indicate the potential of viruses in the water samples especially from the lower catchment areas to infect the human hosts throughout the year. These observations have public health care implications and establish a need to monitor the viral population in addition to traditional water quality indicators. / Thesis (Ph.D.)-University of KwaZulu-Natal, Westville, 2013.

Submitted in partial fulfillment for the Degree of Master of Applied Sciences in Biotechnology, Durban University of Technology, Durban, South Africa, 2017. / The study aims to assess and compare the concentration of microbial contaminants, their sources and distribution in surface water and sediment, and to determine the impact of seasonal variations and corresponding risks of faecal contamination using conventional and molecular methods. Historical data analysis was conducted using E. coli values from the eThekwini Water and Sanitation (EWS) department for 66 months (2009-2014). E. coli and Enterococci were analysed in surface water and sediment samples using the mFC/ spread plate and Colilert-18 (IDEXX) methods. The impact of seasonal variations was assessed using E. coli and Enterococci data collected during rainfall and no rainfall events, using an auto-sampler and sediment trap in parallel. Conventional standard membrane filtration methods using mFC agar, Slanetz & Bartley/ Bile Esculin and Brilliance E. coli selective agar were compared to the enzymatic Colilert-18 and Enterolert (IDEXX) test methods along the Isipingo and Palmiet Rivers. In addition, comparison of the analytical performance of droplet digital PCR (ddPCR) and qPCR for the detection of Salmonella targeting ttr gene in river sediment samples collected from the four sites of the Palmiet River in Durban, South Africa was done. In order to assess the public health risk associated with exposure of men, women and children to microbial pathogens in polluted surface water during recreational activities, the QMRA tool was employed in relation to the risk exposure to pathogenic E. coli, Campylobacter, Salmonella and Shigella. Also, the risk associated with crop irrigation (on farmers) as well as the consumption of crops irrigated with surface water from the Isipingo river was determined. Analysis of the historical data gave a baseline of the two rivers of interest, thus helps understand the current situation of the rivers enabling researchers to pick up potential gaps. In this study after the analysis of the historical data it was evident that at the Palmiet river, microbial analysis must be conducted around the QRI settlements which is a major pollution source. Also, from this study it was found that sampling points situated close to wastewater treatment plants, pump stations or informal settlements were of major concern, thus were considered for the study. It was found that sediment exhibited higher microbial concentrations than surface water, which was observed in both rivers. Also, rainfall had a significant impact on microbial variability. Higher microbial concentrations (indicator organisms) were observed in surface water after a heavy rainfall as appose to when there was no rainfall. This was due to contamination that is washed off into the river and sediment resuspension. Methodology comparison revealed that Colilert-18 and Brilliance E. coli were more selective compared to mFC agar. Brilliance E. coli /Coliform agar was comparable with Colilert-18 IDEXX, which was also observed with Slanetz & Bartley and Enterolert IDEXX. However, when mFC agar was compared with Colilert-18 IDEXX, significant difference was observed. In comparison of two Molecular methods, ddPCR were found to be fully amenable for the quantification of Salmonella and offer robust, accurate, high-throughput, affordable and more sensitive quantitation than qPCR in complex environmental samples like sediments. Quantitative Microbial Risk Assessment (QMRA) relating to recreational and occupational exposure showed that children were at the highest risk of getting infected. Also, it was observed that the probability of infection upon exposure to surface water from the Isipingo and Palmiet rivers was significantly high, hence exceeded the WHO guidelines values. Risk assessment on crops revealed that pathogenic bacteria may pose a risk to the consumer, however, a 9-log reduction may be achieved according to the WHO multi-barrier approach which involves proper washing and proper cooking of the crop before ingestion. Overall the sampling points that had the highest pollution level and constantly exceeded the WHO and DWAF guidelines at the Isipingo river were the points situated and named “Next to the WWTP”, and “Downstream of QRI” at the Palmiet River. / M

M.Sc. (Environmental Management) / The main purpose of this study is to determine whether trends in rainfall patterns correlate to trends in water quality constituents for the Roodeplaat Dam Drainage Basin, thereby increasing the ‘dilution capacity’ potential of the aforementioned water system. The Roodeplaat Dam (reservoir) is a hypertrophic impoundment located approximately 20 kilometres north-east of Pretoria. The dam was originally designed for irrigational purposes and later became an important recreational site. In recent years it serves as an important source for Magalies Water, which represents a state-owned water board that currently supplies potable water to a large area north of Pretoria. The Roodeplaat Dam catchment consists of three contributing rivers to the inflow of the impoundment, namely: The Pienaars River (located in the centre of the catchment), the Edendale Spruit (east of the catchment) and the Moreleta/Hartebees Spruit (west of the catchment). There are also two Water Care Works (Zeekoegat and Baviaanspoort) within the catchment, which supplement additional inputs of treated effluent discharges to the reservoir. Temporal changes in selected physical, chemical and microbial constituents were analysed at established sampling points along each river, including a sample site located at the dam wall outlet. Such changes in water quality, in conjunction with rainfall patterns exhibited in the study area were analysed to determine whether an association exists between the two variables, and more specifically how rainfall impacts on water quality within the catchment which has a direct effect on the quality of the Roodeplaat Dam. Data for rainfall and water quality were analysed over a 10 year period, from January 1999 to December 2009. Water quality sampling results were obtained from the Department of Water Affairs. Rainfall data for the same time period in question was obtained from the South African Weather Service. Results for both variables were projected graphically and collated to determine whether rainfall trends have an impact on concentrations of water quality constituents. Constituent concentrations were also compared at each sample site. To quantitatively justify graphical results, the author preformed Pearson’s and Spearman’s correlation analysis to establish whether rainfall and water quality concentrations displayed significant associations. Results from graphical presentations and quantitative analyses identified that a correlation does exist between rainfall and water quality constituents, whereby an increase in rainfall tends to result in a decrease of water quality constituent concentrations. Microbial constituents contrasted to physical and chemical results, and displayed a strong positive correlation to rainfall. Rainfall therefore increases the ‘dilution capacity’ potential of the catchment, whereby the water system increases in its ability to receive and remove pollutants disposed in them by human induced land-use activities. It was also found from the study that the strength and association between rainfall and water quality constituents is affected by external, anthropogenic variables which also exert an influence on the quality of water present in the Roodeplaat Catchment Area. This includes additional inputs from the Baviaanspoort, which is located along the Pienaars River. Results from the sample site located on this river displayed no relationship for many of the water quality constituents tested. It has also been highlighted from the study how the landscape has been severely altered by the rapid rate of human induced land use activities in the past decade. Further investigations need to incorporate the influences of natural phenomena, such as rainfall, together with influences exerted from anthropogenic activities. This will provide clearer information on the interdependent factors at play which compromise the dilution capacity potential of the Roodeplaat Catchment Area and subsequently the poor water quality status exhibited at the impoundment. Once such externalities are accounted for, it is recommended that a suitable management plan be conducted for the Roodeplaat Catchment Area that is based on scientific grounding and proactively mitigates the impacts exuded by land-use activities, thereby improving the status of the Roodeplaat impoundment.

Biological monitoring and land use data analysis were performed for a small (79,800 acre) watershed in west-central Indiana. A model was developed between Hilsenhoff biotic index and percentage of water (volume) draining through forestland at each sample site (R2.92, P < .002). This water volume model was found to explain more of the variation in biological integrity than USEPA and Ohio EPA habitat assessment methods, as well as, a land use model based upon percentage watershed surface area. Based on this water volume model, maps were created depicting regions within the watershed that had the greatest potential to damage water quality. Land acquisition/conversion projects based upon these maps should improve biological integrity/water quality more efficiently (requiring less land acquisition/conversion, and therefore lowering project costs, while increasing water quality benefits). / Department of Biology

In South Africa water is recognized as a crucial element in the battle against poverty, the cornerstone of prosperity, and a limiting factor to growth. The National Water Act 36 of 1998 recognizes that basic human and environmental needs should be met and that the use of water in all aspects must be sustainable. The Crocodile River (East) is situated in the north east of the Republic of South Africa and it is recognized as a stressed catchment in South Africa. The main impacts are domestic, industrial, agricultural, mining and afforestation activities. These activities pollute the river by discharging effluent as well as seepage from areas that support mining and intensive agriculture in to the river. The river catchment has been a center of research studies for many scientists either focusing on water quality or biological indicators separately. The aim of study was to determine the present ecological condition and the health of the Crocodile River. The objectives were to determine water quality status, identify possible sources of pollution and assess the spatial and temporal trends in ecological state. Fourteen monitoring sites were selected from the Crocodile River and its tributaries. The macro-invertebrates data were collected using the SASS 5 protocol and fish were collected using an electroshocker- catch and release method during high and low flow conditions of the year 2013. Water quality data was obtained by sampling using a polyethylene bottle from different sites within the Crocodile River and its tributaries from September 2012 until August 2013. The samples were analyzed by Mpumamanzi laboratory in Nelspruit and Waterlab in Pretoria. Additional water quality data was obtained from the Department of Water Affairs. Multivariate statistical methods were used to analyze all the data obtained. The multivariate statistical methods indicated that fish and macro-invertebrates species abundance, richness and evenness increase with the river flow distance downstream. Water temperature was one of the leading environmental variables for the structuring of fish and macro-invertebrates assemblage in the Crocodile River and its tributaries. A group formation of site during high and low flow condition by the Bray Curtis similarity and NMDS ordination indicated that many sites share similar macro-invertebrates or fish species. The one way ANOVA analysis indicated that there was no significance difference between macro-invertebrates richness and abundance during both flow conditions but there was a significance difference in fish richness and abundance between the two flow conditions. The PCA indicated that sodium has the highest physico-chemical impact amongst the physico-chemical parameters in the bi-plot followed by ammonium and nitrate. A correlation of physico-chemical parameters such as chlorine, total dissolved solid, electrical conductivity, sulphate and pH was observed. The levels of total dissolved solids and electrical conductivity were found to increase longitudinally as the river flows downstream. The dominance of single species within the macro-invertebrates and fish communities was an indication of imbalance of the communities within the sites. The presence of the macro-invertebrate family Beatidae and the fish species Chiloglanis pretoriae at sites CR3 and CR4 indicates a good water quality in the upper reaches during low flow condition as these species are sensitive to changes in water quality, while the presence of the macro-invertebrate family Pleidea and fish species Barbus viviparus at sites CR10 and KR1 during low flow condition indicated possible water pollution as these species tolerate changes in water quality and this was linked to the discharge of effluent from industrial, abandoned mines and run-offs from agricultural activities in the downstream reaches of the river. The low flow condition was dominated by sensitive species especially in the upper reaches than during high flow condition. The macro-invertebrates assessment index indicated that during low flow condition the Crocodile River was mostly at ecological class B (largely natural with few modification) above the Kwena dam, but from downstream of the dam the ecological category was in C class (moderately modified), while its tributaries are in ecological category B (largely natural with few modification). The fish response assessment index indicated that the ecological category for fish was mostly at C class (moderately modified) in the Crocodile River. The changes in macro-invertebrates communities and fish in the Crocodile River were believed to be associated with change of water quality and habitat modification due to flow modification. Agricultural activities in the upper reaches and a combination of industrial and mining activities in the middle and lower reaches of the Crocodile River were believed to be the sources of pollution that results in the change of water quality, fish and macro-invertebrates assemblage in the Crocodile River. Investing in the health of the Crocodile River is important for many Mbombela citizens and river dwellers as they rely on the functioning of the river for survival. / Environmental Sciences / M. Sc. (Environmental Science)

The aim of this study was to use plants to determine the degree of heavy metal contamination in water and sediments in order to effectively monitor and provide possible recommendation to improve the water quality in the aquatic ecosystem of the Bottelary River.

M.Sc. (Aquatic Health) / Yellowfish and specifically Labeobarbus marequensis are a charismatic species targeted by anglers throughout South Africa. Their population are limited to the north-western parts of the country including the lower reaches of the Crocodile River that flows through the Kruger National Park (KNP). Despite conservation efforts the Crocodile River in the KNP is still highly impacted. The effect of these impacts on the ecosystem is largely unknown. The main aim of the study was to determine the influence of changing water quantity and quality in the Crocodile River on adult L. marequensis. This was achieved by evaluating altered flows (discharge) on the behaviour of adult L. marequensis in the Crocodile River using biotelemetry over a two year period. The influence of altered water quality was assessed using metal bioaccumulation as an indicator of metal exposure in L. marequensis, Clarias gariepinus and Hydrocynus vittatus in the Crocodile and Sabie Rivers during a high and low flow season. Biotelemetry was used on 16 L. marequensis and 12 H. vittatus to determine the habitat use and movement responses of the species. Fish were tagged with Advanced Telemetry Systems (ATS) and Wireless Wildlife (WW) tags and tracked remotely and manually. Home ranges were determined using Arc GIS ®, Habitat uses were analyzed using Windows Excel (© 2011, Microsoft inc.). Environment variables recorded were scored as primary and secondary and then combined with a weighting variable 2:1 ratio (primary variable: secondary variable). A mixed-model analysis of variance (ANOVA) approach with a random co-efficients model and Akaike’s information criteria (AIC) were used to test for significance. Analyses were conducted using SAS version 9 (SAS institute, Cary, NC)...

In South Africa water is recognized as a crucial element in the battle against poverty, the cornerstone of prosperity, and a limiting factor to growth. The National Water Act 36 of 1998 recognizes that basic human and environmental needs should be met and that the use of water in all aspects must be sustainable. The Crocodile River (East) is situated in the north east of the Republic of South Africa and it is recognized as a stressed catchment in South Africa. The main impacts are domestic, industrial, agricultural, mining and afforestation activities. These activities pollute the river by discharging effluent as well as seepage from areas that support mining and intensive agriculture in to the river. The river catchment has been a center of research studies for many scientists either focusing on water quality or biological indicators separately. The aim of study was to determine the present ecological condition and the health of the Crocodile River. The objectives were to determine water quality status, identify possible sources of pollution and assess the spatial and temporal trends in ecological state. Fourteen monitoring sites were selected from the Crocodile River and its tributaries. The macro-invertebrates data were collected using the SASS 5 protocol and fish were collected using an electroshocker- catch and release method during high and low flow conditions of the year 2013. Water quality data was obtained by sampling using a polyethylene bottle from different sites within the Crocodile River and its tributaries from September 2012 until August 2013. The samples were analyzed by Mpumamanzi laboratory in Nelspruit and Waterlab in Pretoria. Additional water quality data was obtained from the Department of Water Affairs. Multivariate statistical methods were used to analyze all the data obtained. The multivariate statistical methods indicated that fish and macro-invertebrates species abundance, richness and evenness increase with the river flow distance downstream. Water temperature was one of the leading environmental variables for the structuring of fish and macro-invertebrates assemblage in the Crocodile River and its tributaries. A group formation of site during high and low flow condition by the Bray Curtis similarity and NMDS ordination indicated that many sites share similar macro-invertebrates or fish species. The one way ANOVA analysis indicated that there was no significance difference between macro-invertebrates richness and abundance during both flow conditions but there was a significance difference in fish richness and abundance between the two flow conditions. The PCA indicated that sodium has the highest physico-chemical impact amongst the physico-chemical parameters in the bi-plot followed by ammonium and nitrate. A correlation of physico-chemical parameters such as chlorine, total dissolved solid, electrical conductivity, sulphate and pH was observed. The levels of total dissolved solids and electrical conductivity were found to increase longitudinally as the river flows downstream. The dominance of single species within the macro-invertebrates and fish communities was an indication of imbalance of the communities within the sites. The presence of the macro-invertebrate family Beatidae and the fish species Chiloglanis pretoriae at sites CR3 and CR4 indicates a good water quality in the upper reaches during low flow condition as these species are sensitive to changes in water quality, while the presence of the macro-invertebrate family Pleidea and fish species Barbus viviparus at sites CR10 and KR1 during low flow condition indicated possible water pollution as these species tolerate changes in water quality and this was linked to the discharge of effluent from industrial, abandoned mines and run-offs from agricultural activities in the downstream reaches of the river. The low flow condition was dominated by sensitive species especially in the upper reaches than during high flow condition. The macro-invertebrates assessment index indicated that during low flow condition the Crocodile River was mostly at ecological class B (largely natural with few modification) above the Kwena dam, but from downstream of the dam the ecological category was in C class (moderately modified), while its tributaries are in ecological category B (largely natural with few modification). The fish response assessment index indicated that the ecological category for fish was mostly at C class (moderately modified) in the Crocodile River. The changes in macro-invertebrates communities and fish in the Crocodile River were believed to be associated with change of water quality and habitat modification due to flow modification. Agricultural activities in the upper reaches and a combination of industrial and mining activities in the middle and lower reaches of the Crocodile River were believed to be the sources of pollution that results in the change of water quality, fish and macro-invertebrates assemblage in the Crocodile River. Investing in the health of the Crocodile River is important for many Mbombela citizens and river dwellers as they rely on the functioning of the river for survival. / Environmental Sciences / M. Sc. (Environmental Science)