In developing countries such as South Africa, diarrhoeal diseases are reported to be linked to inadequate drinking water quality, sanitation, and hygiene behaviours. The consumption of microbiologically contaminated drinking water has been reported to cause diarrhoea, mortality, and morbidity in children under the age of five years. This study evaluated the microbiological pathogens detected in municipal drinking water and diarrhoea trends for children under 5 years of age in South Africa between 2008 and 2018. A trends analysis study was conducted using secondary data on diarrhoea for children under the age of five years and microbial drinking water quality compliance. A negative correlation was found between the occurrence of microbial pathogens in water, morbidity, and mortality rates of children under the age of 5 years in South Africa. As compliance status improved, the mortality rate among children under 5 years old decreased by 31% over the study period. A conclusion can thus be drawn that the microbiological pathogens detected in drinking water at levels complying with SANS 241:2015 Edition 2 standards and diarrhoea incidences were not the primary cause of the mortality of children under 5 years old in South Africa between 2008 and 2018.