Environmental and ecological research has long been characterized as operating along a continuum, with “basic” – representing “investigator-initiated” research – at one end and “applied” – representing “mission-initiated” research – at the other. While federal agency science programs ideally occupy points along this continuum, the resulting science has not always been relevant to solving environmental problems. Here, we suggest that environmental problem-solving by federal agencies has been less effective than it might have been, because of a need for more effective, long-term strategic planning, cooperation across agencies, and incentives for scientists to participate in policy development and implementation. We make suggestions about what federal agencies can do to improve the integration of science, policy, and natural resource management. First, we refer to agency examples, using regulatory (acid deposition) and land management (national forest) issues to illustrate how environmental research intersects with policy development and its implementation. Second, we discuss the barriers that inhibit the application of scientific knowledge in developing and implementing policy – from the perspective of a federal agency and of an individual scientist. Finally, we generate a series of specific recommendations, targeted at federal agencies, individual scientists, and decision makers.