Despite its promise as a potentially beneficial new source of energy, the ocean-based renewable energy industry is still in its infancy, and like any new idea there are many unknowns with the potential to affect both people and our natural environments. A permit for marine renewable energy (MRE) must cut across many sectors of ocean management and serve many masters at once. The permitting process for MRE is where the social and the technical combine, using the best available science to meet the needs and legal requirements of each agency at the table in order to manage both short-term and long-term risk. This research analyzes examples of collaborative marine risk management in practice, when multiple government agencies must work together to identify and manage uncertainty and risk associated with permitting MRE projects in the United States. Two case study projects from Oregon and Maine are examined utilizing semi-structured qualitative interviews with process participants, analysis of relevant project documents, and participant observation of publicly available presentations, workshops, and conferences. This manuscript-style thesis approaches the concepts of risk, uncertainty, and the permitting process for MRE from three distinct angles: 1) characterize the varying perceptions of risk and uncertainty around the permitting table, and what role collaboration plays in the perception and management of risk; 2) evaluate barriers and opportunities in multi-party collaborative permitting arrangements and identify best management practices for future practitioners; and 3) investigate how regulatory perceptions of risk associated with MRE may be affected by the presence of an emergency that incapacitates the regional electrical grid, and how this relates to potential regulatory pathways for emergency MRE project concepts.