A new form of Ecological Risk Assessment aims to improve environmental decision-making through strong stakeholder engagement, often in workshop situations. This wider focus increases interaction between workshop practitioners and stakeholders for reflecting on, and learning from, each others perceptions. In this article, we analyse and discuss a one day workshop that was concerned with trialling this method of deriving an Ecological Risk Assessment. We found that stakeholders had issues with some elements of the workshop process. The decision problem was formulated prior to the workshop and without consultation among all the stakeholders. Consequently, the original decision problem was rejected for a mutually derived broader focus and this resulted in a loss of clarity and purpose. Stakeholders did not wholly concur with the prioritising of ecological values over social and economic values and some stakeholders objected to defining assessment endpoints, because it implies a reductionist approach that doesn't capture significance and understanding of systems. Ecological Risk Assessment workshops are complex and require significant practitioner and stakeholder development to provide useful and mutually derived outcomes.