Inland flooding is one of the most damaging natural hazard events each year in New Hampshire and the United States, the risk of which can be influenced by changes in land use and climate. Initiatives toward climate adaptation are increasingly interested in the use of ecosystem provided capital and infrastructure in preparing for climate impacts such as flooding. While ecosystem-based adaptation offers a new way of responding and preparing for future flood, little is known on how stakeholders perceive ecosystem-based alternatives versus more traditional built options. Through the use of stakeholder engaged decision scenarios and a multi-criteria framework for decision analysis, we aim to understand what drives preferences for flood mitigation and adaptation alternatives and the perceived value of ecosystem-based projects in these selections. This was completed through a four-step process that included: 1) identification of issues and stakeholder groups, 2) stakeholder engagement and value gathering, 3) construction of decision scenarios and project matrices, and 4) workshop implementation and evaluation. We find that attributes of effectiveness and environmental impact are most important to consider in comparing flood mitigation and adaptation alternatives by stakeholders engaged here. While ecosystem services were not always the most highly valued aspects of different alternatives, we found strong preference for some ecosystem-based flood mitigation and adaptation methods such as soft-bank stabilization techniques and wetland conservation. We conclude that for ecosystem-based flood preparation options to be selected at the municipal level, they must be demonstrably effective and technically achievable. Lasting impacts and experiences from recent and highly damaging flood events in New Hampshire and Vermont are thought to be playing determining role in motivating stakeholders to value effectiveness of flood mitigation and adaptation efforts. This methodology is relevant and reproducible for many types of local decision makers across the United States and abroad.