Public health risk assessment of onsite wastewater treatment systems (OWTS) in the city of Port Harcourt, Nigeria and its environs was carried out between the period of August 2012 and April 2013. The objective of the study was to show how the public health risk assessment tool can be used to improve public policies on OWTS. The study involved desk study reviews of the related literature on OWTS, an audit survey of 245 OWTS in the residential area of the city, a public policy survey of OWTS in Port Harcourt city, a public health risk assessment, field observations and investigations. The results revealed that there were no specific policies, legislative and regulatory standards for sustainability of OWTS practice and no risk assessment considerations in the current policy instruments. In general terms, the public policy instruments of OWTS were found to be inadequate for improved and standard system construction, installation, operations and maintenance, compliance, enforcement and inspection. The outcome of the risk map showed widespread and dispersed risk in the use of OWTS.