In this paper, we discuss methods to integrate ecological resources, ecosystem services, risk, and the transition to long-term stewardship on Department of Energy lands. Three types of information are required about ecological resources before decisions can be made about remediation, site transitions, and long-term stewardship: (1) the ecological resources and ecosystem functions (such as productivity) present on site and their spatial pattern, (2) the ecosystem services these resources provide to people, and (3) the risks from the interactions between people and these ecosystems. Once the ecological resources and ecosystem services are evaluated, then decisions about future land use, preservation, conservation, or protection of ecological resources within a designated land use can be implemented. Long-term stewardship requires both ecosystem protection in terms of biological resources and ecosystem function as well as biomonitoring to ensure minimal radiological or chemical risk and to inform future management. In some cases, protection of ecological resources may be preferable to cleanup that is physically disruptive, provided land use designation is consistent with ecological protection. In such instances, less site cleanup can prove preferable to more.