Retrospective ecological risk assessment, restoration, natural resource damage assessment (NRDA) and managing ecosystems all require having a baseline. This policy and practice paper explores the factors that influence baseline selection, and it is suggested that ecological resources would best be served by: (1) integrating NRDA considerations into both future land-use planning and remediation/restoration; (2) selecting a baseline for NRDA that approximates the land-use conditions at the time of occupation (or a preferred ecosystem); and (3) integrating both the positive and negative aspects of industrial occupation into restoration decisions, baseline selection and NRDA. Under the Comprehensive Environmental Response and Compensation and Liability Act (CERCLA), natural resource damages are assessed for injuries incurred since 1980 due to releases, but the release itself may have occurred before 1980. The paper uses the Department of Energy as a case study to examine NRDA and the management of ecosystems. Releases occurred at many DOE sites from the 1950s to the 1980s during nuclear bomb production. It is suggested that the DOE has been responsible not only for injuries to natural resources that occurred as a result of releases, but for significant ecosystem recovery since DOE occupation, because some lands were previously farmed or industrialized. Natural resource injuries due to releases occurred simultaneously with ecosystem recovery that resulted from DOE occupation. While the 1980 date is codified in CERCLA law as the time after which damages can be assessed, baseline can be defined as the conditions the natural resources would have been in today, but for the release of the hazardous substance. It is also suggested that NRDA considerations should be incorporated into the remediation and restoration process at DOE sites, thereby negating the need for formal NRDA following restoration, and reducing the final NRDA costs.