Climate change continues to drive the emergence of infectious diseases, including waterborne zoonoses, by increasing the likelihood of human contact with a reservoir host of microbes previously unknown to humans. Climate change-associated drought deteriorates the environmental water quality by lessening the River's capacity to dilute pollutants and increasing the concentration of pathogenic organisms in freshwater systems. In South Africa, lack of water exacerbated by climate change, including drought, has resulted in instances where people use rivers and source waters of poorer quality. Worse still, humans and livestock share the same source water (surface water), increasing the risk of transmission of zoonoses. Zoonoses are infectious diseases caused by a pathogen that transfers from an animal to a human. The risk of a pandemic occasioned by zoonoses presents a huge threat, from mild to fatal diarrheal illnesses in humans. Rivers contaminated with zoonotic pathogens constitute a significant risk factor. Strategic actions necessary to control the transmission of waterborne zoonoses require background information on factors that drive increased risk of emergence and spread of zoonoses from local freshwater environments. Using a qualitative risk assessment method, this study investigated the likelihood of the emergence and spread of zoonoses from rivers to humans in a typical community with high livestock activity in South Africa. As expected, the study found several context factors driving increased risk of emergence and spread of zoonoses from freshwater environments to humans in South Africa. Given the drought situation of the country and the contribution of identified context factors, one can conclude that the risk of zoonoses emergence and transmission from freshwater systems is high. Concerted environmental surveillance and control have become critical for South Africa.