The identification and quantification of pathogens in raw and treated wastewater is important for monitoring the efficiency of treatment processes. An assessment of the efficacy of wastewater treatment also has implications for influent water quality for drinking water operations. Treated wastewater effluent may harbor infectious pathogenic microorganisms such as enteroviruses, Cryptosporidium and Giardia even after standardized treatment processes. The development of methods to recover Cryptosporidium, Giardia, and enteroviruses from sewage have not been well established. Consequently, detailed investigations of the impact of treated sewage on surface water have not been reported. In this study, ultrafiltration and immunomagnetic separation (IMS) methodologies were optimized to determine and quantify the presence of the target organisms in raw (influent) and treated sewage at three wastewater treatment facilities: Las Cruces, New Mexico; El Paso, Texas; and, Juarez, Mexico. One liter influent grab samples were centrifuged and the pellets were processed by IMS and indirect fluorescent antibody (IFA) for Cryptosporidium and Giardia and the supernatant was processed by ultrafiltration for phage. Raw sewage seeded recoveries of Cryptosporidium and Giardia ranged from 42-81% (SD 3-10) and 27-53% (SD 6-10), respectively (n=3 for each site). The recovery for endogenous phage in raw sewage ranged from 32-50% (SD 10-45) (n=2-4 for each site). Ten liter effluent grab samples were concentrated by ultrafiltration and the pellets were processed by IMS and IFA for Cryptosporidium and Giardia and the supernatant was further concentrated by spin column for phage. Three replicate challenges were done for each site and recoveries of Cryptosporidium and Giardia ranged from 12-25% (SD 4-14) and 1-30% (SD 0.5-21), respectively. Results from this study will help evaluate the impact that treated wastewater may have on pathogen loads in environmental waters. Includes 23 references, tables, figures.