Environmental risk analysts need to draw from a clear typology of uncertainties when qualifying risk estimates and/or significance statements about risk. However, categorisations of uncertainty within existing typologies are largely overlapping, contradictory, and subjective, and many typologies are not designed with environmental risk assessments (ERAs) in mind. In an attempt to rectify these issues, this research provides a new categorisation of uncertainties based, for the first time, on the appraisal of a large subset of ERAs, namely 171 peer-reviewed environmental weight-of-evidence assessments. Using this dataset, a defensible typology consisting of seven types of uncertainty (data, language, system, extrapolation, variability, model, and decision) and 20 related sub-types is developed. Relationships between uncertainties and the techniques used to manage them are also identified and statistically evaluated. A highly preferred uncertainty management option is to take no action when faced with uncertainty, although where techniques are applied they are commensurate with the uncertainty in question. Key observations are applied in the form of guidance for dealing with uncertainty, demonstrated through ERAs of genetically modified higher plants in the EU. The presented typology and accompanying guidance will have positive implications for the identification, prioritisation, and management of uncertainty during risk characterisation.