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Over 25% of the US population and 37% of all new development is served by onsite and small scale wastewater systems, the majority of which rely on percolation of primary treated effluent through soil to achieve purification prior to recharge to the ground water. Attempts to exploit the benefits of decentralized system approaches have resulted in innovations in design approaches and technologies that are emerging at a growing rate. In some cases, modifications to historical practice are warranted and supported by a sound scientific and engineering foundation. In others, design practice has evolved ahead of the knowledge needed to support such change. One such situation concerns the trend where wastewater soil absorption systems (WSAS) are being designed utilizing a higher level of pretreatment than provided by the common septic tank (e.g., sand filter or constructed wetland) to enable elevated hydraulic loading rates and smaller soil treatment systems (either in infiltration area or depth of vadose zone soil). These practices may be sound based on hydraulics, but purification of contaminants of concern, especially pathogenic bacteria and virus has not been proven. This paper discusses the need for a more fundamental understanding of the fate and transport of pathogens in WSASs. The relationship between hydraulic loading rate and quality of applied effluent and their effect on pathogen purification performance is required to utilize soil-aquifer systems effectively while preventing drinking water contamination.