Since 1990, more than 1.8 billion people have gained access to potable water and improved sanitation worldwide. Whilst this represents a vital step towards improving global health and well-being, accelerated population growth coupled with rapid urbanization has further strained existing water supplies. Whilst South Africa aims at spending 0.5% of its GDP on improving sanitation, additional factors such as hydrological variability and growing agricultural needs have further increased dependence on this finite resource. Increasing pressure on existing wastewater treatment plants has led to the discharge of inadequately treated effluent, reinforcing the need to improve and adopt more stringent methods for monitoring discharged effluent and surrounding water sources. This review provides an overview of the relative efficiencies of the different steps involved in wastewater treatment as well as the commonly detected microbial indicators with their associated health implications. In addition, it highlights the need to enforce more stringent measures to ensure compliance of treated effluent quality to the existing guidelines.