Coastal ecosystem management typically relies on subjective interpretation of scientific understanding, with limited methods for explicitly incorporating process knowledge into decisions that must meet multiple, potentially competing stakeholder objectives. Conversely, the scientific community lacks methods for identifying which advancements in system understanding would have the highest value to decision-makers. A case in point is barrier island restoration, where decision-makers lack tools to objectively use system understanding to determine how to optimally use limited contingency funds when project construction in this dynamic environment does not proceed as expected. In this study, collaborative structured decision-making (SDM) was evaluated as an approach to incorporate process understanding into mid-construction decisions and to identify priority gaps in knowledge from a management perspective. The focus was a barrier island restoration project at Ship Island, Mississippi, where sand will be used to close an extensive breach that currently divides the island. SDM was used to estimate damage that may occur during construction, and guide repair decisions within the confines of limited availability of sand and funding to minimize adverse impacts to project objectives. Sand was identified as more limiting than funds, and unrepaired major breaching would negatively impact objectives. Repairing minor damage immediately was determined to be generally more cost effective (depending on the longshore extent) than risking more damage to a weakened project. Key gaps in process-understanding relative to project management were identified as the relationship of island width to breach formation; the amounts of sand lost during breaching, lowering, or narrowing of the berm; the potential for minor breaches to self-heal versus developing into a major breach; and the relationship between upstream nourishment and resiliency of the berm to storms. This application is a prototype for using structured decision-making in support of engineering projects in dynamic environments where mid-construction decisions may arise; highlights uncertainty about barrier island physical processes that limit the ability to make robust decisions; and demonstrates the potential for direct incorporation of process-based models in a formal adaptive management decision framework.