Worldwide, unsustainable use of nature threatens many ecosystems and the services they provide for a broad diversity of life, including humans. Yet, governments commonly claim that the best available science supports their policies governing extraction of natural resources. We confront this apparent paradox by assessing the complexity of the intersections among value judgments, fact claims, and scientifically verified facts. Science can only describe how nature works and predict the likely outcomes of our actions, whereas values influence which actions or objectives society ought to pursue. In the context of natural resource management, particularly of fisheries and wildlife, governments typically set population targets or use quotas. Although these are fundamentally value judgments about how much of a resource a group of people can extract, quotas are often justified as numerical guidance derived from abstracted, mathematical, or theoretical models of extraction. We confront such justifications by examining failures in transparency about value judgments, which may accompany unsupported assertions articulated as factual claims. We illustrate this with two examples. Our first case concerns protection and human use of habitats harboring the northern spotted owl (Strix occidentalis caurina), revealing how biologists and policy scholars have argued for divergent roles of scientists within policy debates, and how debates between scientists engaged in policy-relevant research reveal undisclosed value judgments about communication of science beyond its role as a source of description (observation, measurement, analysis, and inference). Our second case concerns protection and use of endangered gray wolves (Canis lupus) and shows how undisclosed value judgments distorted the science behind a government policy. Finally, we draw from the literature of multiple disciplines and wildlife systems to recommend several improvements to the standards of transparency in applied research in natural resource management. These recommendations will help to prevent value-based distortions of science that can result in unsustainable uses and eventual extinctions of populations. We describe methods for communicating about values that avoid commingling factual claims and discuss approaches to communicating science that do not perpetuate the misconception that science alone can dictate policy without consideration of values. Our remedies can improve transparency in both expert and public debate about preserving and using natural resources, and thereby help prevent non-human population declines worldwide.