Deteriorating ground-water quality has stimulated new research initiatives; that, in part focus on the subsurface fate and transport behavior of pathogens. Increasing application of aquifer storage and recovery (ASR) operations has brought the issue of fate and transport of microbial pathogens into sharper focus. Because ASR practices are becoming widespread, they are found within diverse geohydrologic regimes. This is coupled with modest, recent regulatory guidance and limited understanding of how pathogens within the subsurface are affected by this type of water handling. These factors make the study of pathogen fate and transport within ASR systems extremely difficult. A major challenge in assessing the utility of ASR is to identify the pathogens that may pose a threat in each ASR setting. Another concern is how best to study the role of pathogens upon water quality during ASR operations.