Like the Stage 1 Disinfectants/Disinfection Byproducts Rule, the Interim Enhanced Surface Water Treatment Rule (IESWTR) grew out of the negotiated rulemaking the US Environmental Protection Agency convened in 1992-93 under the Federal Advisory Committee Act (FACA). The rulemaking sought to develop a consensus approach to simultaneously addressing potential health risks posed by disinfection by-products (DBPs) and waterborne pathogens. Even though the process was complicated by the possibility of making inadvertent risk-risk tradeoffs between protection from DBPs and protection from pathogens and uncertainties affecting the assessment of both risks, the regulatory-negotiations committee was able to devise a well-balanced, staged approach to regulation. A second FACA committee finalized the approach in 1996-97. This article summarizes the microbial side of the benefit-cost analysis and the explicit uncertainty analysis that was used to inform the stakeholders and the negotiators. Includes 21 references, tables, figures.