Aquatic non-indigenous species (ANS) management employs risk assessment as a tool to prioritize prevention and control efforts, but timely and comprehensive risk estimates are difficult due to various sources of uncertainty, particularly knowledge gaps. Several fields use or endorse the use of precaution, as well as group Delphic processes, to mitigate this uncertainty. To test the application of these methods in ANS risk assessment, we surveyed the knowledge and attitudes held by ANS scientists and managers regarding uncertainty and involved these experts in a modified Delphic process to determine consequence for a suite of 10 ANS. We found that participants supported the application of precaution in risk assessments. We also found the Delphic process aided the risk assessment process by facilitating outcomes that are supported by experts and stakeholders involved, account for uncertainty, and are therefore useful for policy and management purposes. Finally, we provide several recommendations for mitigating uncertainty in consequence assessments. These outcomes and recommendations provide increased understanding of the presence and sources of uncertainty, and the potential use of precaution and Delphic processes to facilitate the completion of comprehensive biosecurity risk assessments, despite the challenges posed by existing knowledge gaps in ANS impact information.