This study aims to evaluate the removal efficiency of microbial contaminants from two hospitals on-site Wastewater Treatment Plants (WWTPs) in Saudi Arabia. Hospital wastewaters often go untreated in Saudi Arabia as in many devolving countries, where no specific regulations are imposed regarding hospital wastewater treatment. The current guidelines are placed to ensure a safe treated wastewater quality, however, they do not regulate for pathogenic bacteria and emerging contaminants. Results from this study have detected pathogenic bacterial genera and antibiotic resistant bacteria in the sampled hospitals wastewater. And although the treatment process of one of the hospitals was able to meet current quality guidelines, the other hospital treatment process failed to meet these guidelines and disgorge of its wastewater might be cause for concern. In order to estimate the risk to the public health and the impact of discharging the treated effluent to the public sewage, a comprehensive investigation is needed that will facilitate and guide suggestions for more detailed guidelines and monitoring.