The practice of chlorine disinfection of drinking water to reduce microbial risks provides substantial benefits to public health. However, increasing concern around potential risks of cancer associated with exposure to chlorinated disinfection byproducts confuses this issue. This article examines the science agenda regarding chlorinated disinfection byproducts (CDBP) and cancer in Canada and the United States, focusing on the social construction of scientific knowledge claims and evidence. Data for this analysis were obtained from published documents as well as from in‐depth interviews with epidemiologists and toxicologists centrally involved with the issue in both countries. Results of the analysis suggest that toxicological scientists want to close the door on the “chloroform issue” due to increasing evidence that chloroform is safe at low doses, because epidemiological scientists can no longer move forward the cancer science until significant improvements can be made in assessing human exposures, and because the scientific foci of research on DBP have shifted accordingly. Further, a distinction emerges in terms of how scientific uncertainties are interpreted when they cross‐cut disciplines in the context of human health risk assessment. We suggest this tension reflects a balance of how uncertainty and authorities are managed in a mandated science‐policy domain. Sufficient evidence was provided to keep the DBP issue on the regulatory agenda and to generate additional research, yet authorities and concomitant interpretations of uncertainty were contested. Such science generation and contestation inevitably influences complex risk assessment processes with respect to what water‐related health risks are addressed and how.