More than 50 years of research, development, manufacture, and testing of nuclear weapons at Department of Energy (DOE) sites has left a legacy of on-site contamination that often spreads to surrounding areas. Despite substantial cleanup budgets in the last decade, the DOE's top-to-bottom review team concluded that relatively little actual cleanup has been accomplished, although milestones have been met and work packages completed. Rather than solely use regulatory constraints to direct cleanup, many people have suggested that human and ecological health should guide long-term stewardship goals of DOE-managed sites. The main questions are how ecological and human health considerations should be applied in deciding the extent of cleanup that contaminated sites should receive and how near-term and longer run considerations of costs and benefits should be balanced as cleanup decisions are made. One effort to protect ecological integrity is the designation of the largest sites as National Environmental Research Parks (NERPs). Recently, the Competitive Enterprise Institute (CEI) suggested isolating and conserving DOE sites as a policy priority because of their rich ecological diversity. A more effective long-term stewardship approach for former nuclear weapons complex sites may emerge if the guiding principles are to (1) reduce risks to human and ecological health, (2) protect cultural traditions, and (3) lower short- and long-term cleanup and remediation costs. A "net benefits" perspective that takes both near- and longer-term costs and consequences into account can help illuminate the trade-offs between expensive cleanup in the near term and the need to assure long-term protection of human health, cultural values, and high levels of biodiversity and ecological integrity that currently exist at many DOE sites.