Assessment of ecosystem change often focuses on the degree of conversion and representation in networks of protected areas. While essential, these factors alone do not provide a holistic index of ecosystem conditions. Metrics that compare the current state of ecosystems to a meaningful reference condition can help identify “hidden” risks, lost functions, and provide conservation and management-relevant insights. Here we review a departure metric that can be used to measure ecosystem conditions and its implementation for all lands in the United States by the LANDFIRE Program. We then use two case studies to demonstrate how manually calculating the departure metric is used to explore under- and over-representation of structural stages. Finally, we document the assumptions, interpretation, and limitations of the departure metric, and discuss its current and possible future applications.