Water shortage in South Africa is a mixture of many factors: limited and highly polluted watercourses, low rainfall, fast growing population and high evaporation rates. Many studies on watercourses have shown a decline on quality due to the ongoing pollution caused by urbanization, mining, industry, power generation, afforestation and agriculture. Given the current forecasts based on population growth versus the country’s limited water resources, it is unlikely to keep existing patterns regarding the use of water and the discharge of wastes. Predictions are also indicating that pollutants will continue to accumulate in freshwater resources independently of the population growth in South Africa. Issues associated with water quality can turn out to be worsened with environmental devastating consequences. For instance, in the agricultural sector it may lead to a drop in yields and quality for fruits and crops followed by soil contamination. It can harmfully affect the population and aquatic health. Furthermore, water quality deterioration can affect the costs related to purification processes resulting in an increased price of clean water. Human induced activities causing salinization, eutrophication, acidification, presence of pathogens in watercourses, inappropriate waste discharge practices and sewage spills are major causes influencing or deteriorating water quality in South Africa.