Over the past decade, ocean acidification (OA) has emerged as a major concern in ocean science. The field of OA is based on certainties—uptake of carbon dioxide into the global ocean alters its carbon chemistry, and many marine organisms, especially calcifiers, are sensitive to this change. However, the field must accommodate uncertainties about the seriousness of these impacts as it synthesizes and draws conclusions from multiple disciplines. There is pressure from stakeholders to expeditiously inform society about the extent to which OA will impact marine ecosystems and the people who depend on them. Ultimately, decisions about actions related to OA require evaluating risks about the likelihood and magnitude of these impacts. As the scientific literature accumulates, some of the uncertainty related to single-species sensitivity to OA is diminishing. Difficulties remain in scaling laboratory results to species and ecosystem responses in nature, though modeling exercises provide useful insight. As recognition of OA grows, scientists’ ability to communicate the certainties and uncertainties of our knowledge on OA is crucial for interaction with decision makers. In this regard, there are a number of valuable practices that can be drawn from other fields, especially the global climate change community. A generally accepted set of best practices that scientists follow in their discussions of uncertainty would be helpful for the community engaged in ocean acidification.