This special report summarizes the activities of the Ecological Habitat Modeling Workshop held April 11–12, 2019, at the US Fish and Wildlife Service (USFWS) Blackwater National Wildlife Refuge Visitors Center in Cambridge, Maryland. The workshop guided 21 participants through the process of conceptualizing, quantifying, evaluating, and communicating ecological responses to inform guidance and management decisions for ecological restoration projects. Working in interactive groups, participants used the restoration work already in progress at nearby Swan Island as the basis for their model development. Over the course of the two-day workshop, participants learned the mechanics and challenges of applying modeling processes to shape the restoration of dynamic ecosystems. Through group work and brainstorming, they identified a number of benchmarks to assess restoration success and future resilience. To accommodate the changeable and often unpredictable natural events that can shape ecosystems, workshop facilitators emphasized building iterative, fluid ecological habitat models. Next steps include publishing this special report and scheduling a follow-up workshop that will include a site visit to Swan Island.