Policy and research issues in the framing and qualities of uncertainties in risks are analyzed, based on the assessments of dioxin-like compounds (DLCs) and other ingredients in Baltic Sea fish, a high-profile case of governance. Risks are framed broadly, to then focus on dioxins and beneficial fatty acids, fish consumption, human health, and science-management links. Hierarchies of uncertainty (data, model, decision rule, and epistemic) and ambiguity (of values) are used to identify issues of scientific and policy contestation and opportunities for resolving them. The associated complexity of risks is illustrated by risk—benefit analyses of fish consumption and by evaluations of guideline values, highlighting value contents and policy factors in presumably scientific decision criteria, and arguments used in multi-dimensional risk and benefit comparisons. These comparisons pose challenges to narrow assessments centered, for e.g., on toxicants or on food benefits, and to more many-sided and balanced risk communication and management. It is shown that structured and contextualized treatment of uncertainties and ambiguities in a reflexive approach can inform balances between wide and narrow focus, detail and generality, and evidence and precaution.