Prioritizing and assessing risks associated with chemicals, industrial materials, or emerging technologies is a complex problem that benefits from the involvement of multiple stakeholder groups. For example, in the case of engineered nanomaterials (ENMs), scientific uncertainties exist that hamper environmental, health, and safety (EHS) assessments. Therefore, alternative approaches to standard EHS assessment methods have gained increased attention. The objective of this paper is to describe the application of a web-based, interactive decision support tool developed by the U.S. Environmental Protection Agency (U.S. EPA) in a pilot study on ENMs. The piloted tool implements U.S. EPA's comprehensive environmental assessment (CEA) approach to prioritize research gaps. When pursued, such research priorities can result in data that subsequently improve the scientific robustness of risk assessments and inform future risk management decisions. Pilot results suggest that the tool was useful in facilitating multi-stakeholder prioritization of research gaps. Results also provide potential improvements for subsequent applications. The outcomes of future CEAWeb applications with larger stakeholder groups may inform the development of funding opportunities for emerging materials across the scientific community (e.g., National Science Foundation Science to Achieve Results [STAR] grants, National Institutes of Health Requests for Proposals).