The U.S. Environmental Protection Agency’s (EPA) Water Laboratory Alliance relies on the Centers for Disease Control and Prevention’s ultrafiltration-based Water Processing Procedure (WPP) for concentration of biosafety level 3 (BSL-3) agents from 10 L to 100 L of drinking water. The WPP requires comprehensive training and practice to maintain proficiency, resulting in a critical need for quality control (QC) criteria. The aim of this study was to develop criteria using male-specific (MS2) coliphage (BSL-2 agent) to minimize safety hazards associated with BSL-3 agents and to use the criteria to evaluate analytical proficiency during a demonstration exercise. EPA Method 1602 with EasyPhage was used during the study to develop QC criteria for 100-mL, and 40–100 L samples. The demonstration exercise indicated that the MS2 criteria would allow laboratories to demonstrate proficiency using the WPP with 40–100 L samples. In addition, the QC criteria developed for 100-mL samples has broad applicability at laboratories that are using MS2 for other types of analyses, such as assessment of water treatment devices. The development of MS2 QC criteria allows laboratories to develop and confirm ongoing proficiency using the WPP.