Many countries are faced with monumental cleanup tasks remaining from World War II and the Cold War and consistent methodologies are essential to assess the risk from pollutants and the risk from cleanup. In the USA, the Department of Energy (DOE), and other federal and state agencies need to be able to rapidly evaluate the risk to ecological resources for remediation projects. While ecological risk assessments for radionuclides and other contaminants can be performed for different species, evaluations of species assemblages, communities, and ecosystems is more difficult. We summarize an evaluation method for ecological resources on individual remediation units that will allow comparison among a large number of units and that can be modified and applied to the DOE complex-wide. We evaluated the deactivation and decommissioning (D & D) facilities at the Hanford site as case studies. Remediation of these sites has the potential to provide harm to, or increase the value of, ecological resources during and after the process. The evaluation method includes three categories: (1) general steps, (2) ecological descriptions, and (3) ecological ratings. The general steps include identifying the categories of resources (level of resource value), identifying the units to be evaluated (e.g., remediation units), identifying a reasonable ecological buffer around the evaluation units, identifying the remediation options (from milestones or other agreements), and developing a rating scale. Ecological descriptions include identifying previous ecological values of specific areas on the evaluation unit, conducting field studies to assess the current conditions, and summarizing the percent of each resource value on the evaluation unit and buffer area. The ecological risk of harm is determined by using the rating scale to evaluate the potential harm to the ecological (and eco-cultural) resources on each evaluation unit currently, during remediation, and in the post-remediation phase. Currently, the risks (potential harm) to ecological resources on the D & D facilities at the Hanford site are non-discernible, but they increase to very high (for reactors) during remediation when there is physical disruption, increased traffic and personnel, and possible increased contamination. Following remediation, the potential harm to ecological resources is low, and the value may be increased due to restoration of native vegetation on sites that were largely industrial prior to remediation. These methods provide managers, regulators, tribes, and the general public with assurance that ecological and eco-cultural resources and the environment are being protected during and following remediation.